2PA8 | pdb_00002pa8

X-Ray Crystal Structure of the D/L Subcomplex of the Sulfolobus Solfataricus RNA polymerase

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth L]	SCOP2 Family	RBP11/RpoL	8080731	4003562	SCOP2 (2022-06-29)
B [auth L]	SCOP2 Superfamily	RBP11-like subunits of RNA polymerase	8080732	3001655	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth D]	RNA_pol_L	e2pa8D1	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)
A [auth D]	RNA_pol_A_bac_1	e2pa8D2	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)
B [auth L]	RNA_pol_L_2	e2pa8L1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A [auth D]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
A [auth D]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B [auth L]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D]	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
A [auth D]	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
B [auth L]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D]	DNA-directed RNA polymerase subunit D	DNA binding binding nucleic acid binding 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	-	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
B [auth L]	DNA-directed RNA polymerase subunit L	DNA binding binding nucleic acid binding protein binding protein dimerization 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
A [auth D]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A [auth D]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A [auth D]	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
A [auth D]	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
A [auth D]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A [auth D]	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
A [auth D]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
B [auth L]	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
B [auth L]	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
B [auth L]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
B [auth L]	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.