4V8S

Archaeal RNAP-DNA binary complex at 4.32Ang

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth AI]	SCOP2B Superfamily	RPB6/omega subunit-like	8078379	3000189	SCOP2B (2022-06-29)
X [auth BK]	SCOP2B Superfamily	RPB6/omega subunit-like	8078379	3000189	SCOP2B (2022-06-29)
BA [auth BQ]	SCOP2B Superfamily	RNA polymerase subunit 13, Rpo13-like	8093029	3002666	SCOP2B (2022-06-29)
D [auth AJ]	SCOP2B Superfamily	RNA polymerase subunit 13, Rpo13-like	8093029	3002666	SCOP2B (2022-06-29)
E [auth AM]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8080734	3001655	SCOP2B (2022-06-29)
Y [auth BL]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8080734	3001655	SCOP2B (2022-06-29)
F [auth AO]	SCOP2B Superfamily	RNA polymerase subunit RPB10	8063362	3001213	SCOP2B (2022-06-29)
Z [auth BN]	SCOP2B Superfamily	RNA polymerase subunit RPB10	8063362	3001213	SCOP2B (2022-06-29)
G [auth AR]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8073729	3001330	SCOP2B (2022-06-29)
G [auth AR]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8073729	3001330	SCOP2B (2022-06-29)
Q [auth BB]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8073729	3001330	SCOP2B (2022-06-29)
Q [auth BB]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8073729	3001330	SCOP2B (2022-06-29)
J [auth AU]	SCOP2B Superfamily	HRDC-like	8086301	3000132	SCOP2B (2022-06-29)
U [auth BF]	SCOP2B Superfamily	HRDC-like	8086301	3000132	SCOP2B (2022-06-29)
K [auth AV]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093394	3002702	SCOP2B (2022-06-29)
K [auth AV]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093033	3002702	SCOP2B (2022-06-29)
V [auth BG]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093033	3002702	SCOP2B (2022-06-29)
V [auth BG]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093394	3002702	SCOP2B (2022-06-29)
O [auth AZ]	SCOP2B Superfamily	RPB5-like RNA polymerase subunit	8063566	3001722	SCOP2B (2022-06-29)
W [auth BH]	SCOP2B Superfamily	RPB5-like RNA polymerase subunit	8063566	3001722	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth AI]	RNA_pol_Rpb6_1	e4v8sAI1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
X [auth BK]	RNA_pol_Rpb6_1	e4v8sBK1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
BA [auth BQ]	RNA_pol_Rpo13	e4v8sBQ1	A: alpha bundles	X: YqgQ-like (From Topology)	H: YqgQ-like (From Topology)	T: YqgQ-like	F: RNA_pol_Rpo13	ECOD (1.6)
D [auth AJ]	RNA_pol_Rpo13	e4v8sAJ1	A: alpha bundles	X: YqgQ-like (From Topology)	H: YqgQ-like (From Topology)	T: YqgQ-like	F: RNA_pol_Rpo13	ECOD (1.6)
E [auth AM]	RNA_pol_L_2	e4v8sAM1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
Y [auth BL]	RNA_pol_L_2	e4v8sBL1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
F [auth AO]	RNA_pol_N	e4v8sAO1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
Z [auth BN]	RNA_pol_N	e4v8sBN1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
G [auth AR]	RNA_pol_Rpb2_6_3rd_2	e4v8sAR7	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
G [auth AR]	RNA_pol_Rpb2_6_2nd_1	e4v8sAR1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
G [auth AR]	RNA_pol_Rpb2_3	e4v8sAR3	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
G [auth AR]	RNA_pol_Rpb2_1	e4v8sAR2	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
G [auth AR]	RNA_pol_Rpb2_45_1	e4v8sAR5	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
G [auth AR]	RNA_pol_Rpb2_7	e4v8sAR6	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
G [auth AR]	RNA_pol_Rpb2_4	e4v8sAR4	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
Q [auth BB]	RNA_pol_Rpb2_6_3rd_2	e4v8sBB6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
Q [auth BB]	RNA_pol_Rpb2_6_2nd_1	e4v8sBB2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
Q [auth BB]	RNA_pol_Rpb2_3	e4v8sBB3	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
Q [auth BB]	RNA_pol_Rpb2_1	e4v8sBB7	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
Q [auth BB]	RNA_pol_Rpb2_45_1	e4v8sBB5	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
Q [auth BB]	RNA_pol_Rpb2_7	e4v8sBB1	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
Q [auth BB]	RNA_pol_Rpb2_4	e4v8sBB4	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
H [auth AS]	RNA_pol_L	e4v8sAS1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L	ECOD (1.6)
H [auth AS]	RNA_pol_A_bac_1	e4v8sAS2	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
S [auth BD]	RNA_pol_L	e4v8sBD2	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L	ECOD (1.6)
S [auth BD]	RNA_pol_A_bac_1	e4v8sBD1	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
I [auth AT]	S1_1	e4v8sAT2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
I [auth AT]	SHS2_Rpb7-N	e4v8sAT1	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: SHS2_Rpb7-N	ECOD (1.6)
T [auth BE]	S1_1	e4v8sBE2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
T [auth BE]	SHS2_Rpb7-N	e4v8sBE1	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: SHS2_Rpb7-N	ECOD (1.6)
J [auth AU]	RNA_pol_Rpb4	e4v8sAU1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
U [auth BF]	RNA_pol_Rpb4	e4v8sBF1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
K [auth AV]	RNA_pol_RpbG	e4v8sAV1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_RpbG	ECOD (1.6)
V [auth BG]	RNA_pol_RpbG	e4v8sBG1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_RpbG	ECOD (1.6)
L [auth AW]	RNA_pol_Rpb1_2	e4v8sAW4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
L [auth AW]	RNA_pol_Rpb1_1	e4v8sAW1	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
L [auth AW]	RNA_pol_Rpb1_4	e4v8sAW3	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
L [auth AW]	RNA_pol_Rpb1_3	e4v8sAW2	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)
P [auth BA]	RNA_pol_Rpb1_2	e4v8sBA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
P [auth BA]	RNA_pol_Rpb1_1	e4v8sBA1	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
P [auth BA]	RNA_pol_Rpb1_4	e4v8sBA2	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
P [auth BA]	RNA_pol_Rpb1_3	e4v8sBA3	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)
AA [auth BP]	DNA_RNApol_7kD	e4v8sBP1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)
M [auth AX]	DNA_RNApol_7kD	e4v8sAX1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)
N [auth AY]	RNAP_A''	e4v8sAY2	A: a+b two layers	X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_A''	ECOD (1.6)
N [auth AY]	RNAP_II_Rpb1_C	e4v8sAY1	A: a+b two layers	X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_II_Rpb1_C	ECOD (1.6)
N [auth AY]	RNA_pol_Rpb1_5_3rd	e4v8sAY3	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
N [auth AY]	PRK04309_like_1	e4v8sAY4	A: a+b complex topology	X: helical domain in yeast RNA-polymerases	H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)	T: third helical domain in yeast RNA-polymerase II beta-prime subunit	F: PRK04309_like_1	ECOD (1.6)
R [auth BC]	RNAP_A''	e4v8sBC2	A: a+b two layers	X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_A''	ECOD (1.6)
R [auth BC]	RNAP_II_Rpb1_C	e4v8sBC1	A: a+b two layers	X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_II_Rpb1_C	ECOD (1.6)
R [auth BC]	RNA_pol_Rpb1_5_3rd	e4v8sBC4	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
R [auth BC]	PRK04309_like_1	e4v8sBC3	A: a+b complex topology	X: helical domain in yeast RNA-polymerases	H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)	T: third helical domain in yeast RNA-polymerase II beta-prime subunit	F: PRK04309_like_1	ECOD (1.6)
O [auth AZ]	RNA_pol_Rpb5_C	e4v8sAZ1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
W [auth BH]	RNA_pol_Rpb5_C	e4v8sBH1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth AI], X [auth BK]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
E [auth AM], Y [auth BL]	PF13656	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.	Domain
F [auth AO], Z [auth BN]	PF01194	RNA polymerases N / 8 kDa subunit (RNA_pol_N)	RNA polymerases N / 8 kDa subunit	-	Domain
G [auth AR], Q [auth BB]	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
G [auth AR], Q [auth BB]	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
G [auth AR], Q [auth BB]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
G [auth AR], Q [auth BB]	PF04566	RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)	RNA polymerase Rpb2, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].	Domain
G [auth AR], Q [auth BB]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
G [auth AR], Q [auth BB]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
G [auth AR], Q [auth BB]	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].	Domain
H [auth AS], S [auth BD]	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
H [auth AS], S [auth BD]	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain
I [auth AT], T [auth BE]	PF03876	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].	Domain
I [auth AT], T [auth BE]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
J [auth AU], U [auth BF]	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family
K [auth AV], V [auth BG]	PF16992	DNA-directed RNA polymerase, subunit G (RNA_pol_RpbG)	DNA-directed RNA polymerase, subunit G	-	Family
L [auth AW], P [auth BA]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
L [auth AW], P [auth BA]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
L [auth AW], P [auth BA]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
L [auth AW], P [auth BA]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
L [auth AW], P [auth BA]	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
N [auth AY], R [auth BC]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
O [auth AZ], W [auth BH]	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AC], CA [auth BR]	5'-D(TPCPTPTPAPTPAPCPTPCPTPAPTPCP)-3'	-	-	-
B [auth AD], DA [auth BS]	5'-D(APTPAPGPAPGPTPAPTPAPAPGPAPTP APG)-3'	-	-	-
C [auth AI], X [auth BK]	DNA-DIRECTED RNA POLYMERASE SUBUNIT K	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA polymerase III activity RNA polymerase I activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process tRNA transcription tRNA transcription by RNA polymerase III RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process tRNA transcription tRNA transcription by RNA polymerase III metabolic process cellular process macromolecule metabolic process transcription by RNA polymerase III	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
BA [auth BQ], D [auth AJ]	RNA POLYMERASE SUBUNIT 13	DNA binding binding organic cyclic compound binding nucleic acid binding RNA polymerase binding protein binding enzyme binding transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	-	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
E [auth AM], Y [auth BL]	DNA-DIRECTED RNA POLYMERASE SUBUNIT L	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
F [auth AO], Z [auth BN]	DNA-DIRECTED RNA POLYMERASE SUBUNIT N	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
G [auth AR], Q [auth BB]	DNA-DIRECTED RNA POLYMERASE	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
H [auth AS], S [auth BD]	DNA-DIRECTED RNA POLYMERASE SUBUNIT D	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups iron-sulfur cluster binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups iron-sulfur cluster binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding protein binding protein dimerization activity cation binding ion binding metal ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
I [auth AT], T [auth BE]	RNA POLYMERASE SUBUNIT 7	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
J [auth AU], U [auth BF]	RNA POLYMERASE SUBUNIT 4	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
K [auth AV], V [auth BG]	RNA POLYMERASE SUBUNIT 8	DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
L [auth AW], P [auth BA]	DNA-DIRECTED RNA POLYMERASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transition metal ion binding zinc ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
AA [auth BP], M [auth AX]	DNA-DIRECTED RNA POLYMERASE SUBUNIT P	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
N [auth AY], R [auth BC]	DNA-DIRECTED RNA POLYMERASE SUBUNIT A''	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
O [auth AZ], W [auth BH]	DNA-DIRECTED RNA POLYMERASE SUBUNIT H	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase II activity RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA polymerase III activity RNA polymerase I activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth AI], X [auth BK]	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
C [auth AI], X [auth BK]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
C [auth AI], X [auth BK]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
C [auth AI], X [auth BK]	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
BA [auth BQ], D [auth AJ]	IPR021985	RNA polymerase Rpo13 subunit HTH domain	Domain
E [auth AM], Y [auth BL]	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
E [auth AM], Y [auth BL]	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
E [auth AM], Y [auth BL]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
E [auth AM], Y [auth BL]	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
F [auth AO], Z [auth BN]	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
F [auth AO], Z [auth BN]	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
F [auth AO], Z [auth BN]	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
G [auth AR], Q [auth BB]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
G [auth AR], Q [auth BB]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
G [auth AR], Q [auth BB]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
G [auth AR], Q [auth BB]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
G [auth AR], Q [auth BB]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
G [auth AR], Q [auth BB]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
G [auth AR], Q [auth BB]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
G [auth AR], Q [auth BB]	IPR007646	RNA polymerase Rpb2, domain 4	Domain
G [auth AR], Q [auth BB]	IPR007647	RNA polymerase Rpb2, domain 5	Domain
G [auth AR], Q [auth BB]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
G [auth AR], Q [auth BB]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
G [auth AR], Q [auth BB]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
G [auth AR], Q [auth BB]	IPR019969	DNA-directed RNA polymerase subunit Rpo2	Family
H [auth AS], S [auth BD]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
H [auth AS], S [auth BD]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
H [auth AS], S [auth BD]	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
H [auth AS], S [auth BD]	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
H [auth AS], S [auth BD]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
H [auth AS], S [auth BD]	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
H [auth AS], S [auth BD]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
I [auth AT], T [auth BE]	IPR046399	DNA-directed RNA polymerase subunit Rpo7	Family
I [auth AT], T [auth BE]	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
I [auth AT], T [auth BE]	IPR004519	DNA-directed RNA polymerase, subunit E/RPC8	Family
I [auth AT], T [auth BE]	IPR003029	S1 domain	Domain
I [auth AT], T [auth BE]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
I [auth AT], T [auth BE]	IPR045113	RNA polymerase subunit Rpb7-like	Family
I [auth AT], T [auth BE]	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
J [auth AU], U [auth BF]	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
J [auth AU], U [auth BF]	IPR044876	HRDC domain superfamily	Homologous Superfamily
J [auth AU], U [auth BF]	IPR010997	HRDC-like superfamily	Homologous Superfamily
J [auth AU], U [auth BF]	IPR010924	DNA-directed RNA polymerase subunit Rpo4	Family
K [auth AV], V [auth BG]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
K [auth AV], V [auth BG]	IPR031555	DNA-directed RNA polymerase subunit Rpo8	Family
L [auth AW], P [auth BA]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
L [auth AW], P [auth BA]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
L [auth AW], P [auth BA]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
L [auth AW], P [auth BA]	IPR012758	DNA-directed RNA polymerase subunit Rpo1N	Family
L [auth AW], P [auth BA]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
L [auth AW], P [auth BA]	IPR000722	RNA polymerase, alpha subunit	Domain
L [auth AW], P [auth BA]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
L [auth AW], P [auth BA]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
L [auth AW], P [auth BA]	IPR006592	RNA polymerase, N-terminal	Domain
L [auth AW], P [auth BA]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
AA [auth BP], M [auth AX]	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
AA [auth BP], M [auth AX]	IPR023464	DNA-directed RNA polymerase subunit Rpo12	Family
AA [auth BP], M [auth AX]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
N [auth AY], R [auth BC]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
N [auth AY], R [auth BC]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
N [auth AY], R [auth BC]	IPR012757	DNA-directed RNA polymerase subunit Rpo1C	Family
O [auth AZ], W [auth BH]	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
O [auth AZ], W [auth BH]	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
O [auth AZ], W [auth BH]	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
O [auth AZ], W [auth BH]	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site

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4V8S

Archaeal RNAP-DNA binary complex at 4.32Ang

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage