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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "secE"

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Search Summary

This query matches 28 Structures.

Refinements

Structure Determination Methodology

experimental (28)

Scientific Name of Source Organism

	Geobacillus thermodenitrificans NG80-2 (10)
	Bacillus subtilis subsp. subtilis str. 168 (9)
	Escherichia coli (8)
	Escherichia coli K-12 (4)
	Lama glama (4)
	Methanocaldococcus jannaschii (4)
	Saccharomyces cerevisiae (4)
	Aequorea victoria (3)
	Thermus thermophilus HB8 (2)
	synthetic construct (2)

More...

Taxonomy

	Bacteria (19)
	Eukaryota (9)
	Archaea (6)
	other sequences (2)

Experimental Method

	ELECTRON MICROSCOPY (14)
	X-RAY DIFFRACTION (14)

Polymer Entity Type

	Protein (28)
	DNA (4)
	RNA (2)

Refinement Resolution (Å)

	2.0 - 2.5 (3)
	2.5 - 3.0 (4)
	3.0 - 3.5 (7)
	3.5 - 4.0 (7)
	> 4.5 (7)

Release Date

	2000 - 2004 (3)
	2005 - 2009 (8)
	2010 - 2014 (2)
	2015 - 2019 (7)
	2020 - 2024 (2)
	2025 - 2029 (6)

Enzyme Classification Name

	Translocases (11)
	Hydrolases (5)

Membrane Protein Annotation

	PDBTM (23)
	MemProtMD (18)
	OPM (14)
	mpstruc (12)

Symmetry Type

Asymmetric (28)

SCOP Classification

	Membrane and cell surface proteins and peptides (7)
	All alpha proteins (1)
	Alpha and beta proteins (a/b) (1)
	Alpha and beta proteins (a+b) (1)
	Artifacts (1)

AllSelected

1 to 25 of 28 Structures

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1R7M \| pdb_00001r7m	Download File View File

The homing endonuclease I-SceI bound to its DNA recognition region

Moure, C.M., Gimble, F.S., Quiocho, F.A.

(2003) J Mol Biology 334: 685-695

Released	2004-10-26
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Intron-encoded endonuclease I-SceI (protein) 5'-D(CPAPCPGPCPTPAPGPGPGPAPTPAPAPCPAPGPGPGPTPAPAPTPAPC)-3' (nucleic acid) 5'-D(GPGPTPAPTPTPAPCPCPCPTPGPTPTPAPTPCPCPCPTPAPGPCPGPT)-3' (nucleic acid)
Unique Ligands	CA

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1RH5 \| pdb_00001rh5	Download File View File

The structure of a protein conducting channel

van den Berg, B., Clemons Jr., W.M., Collinson, I., Modis, Y., Hartmann, E., Harrison, S.C., Rapoport, T.A.

(2004) Nature 427: 36-44

Released	2004-01-06
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Preprotein translocase secE subunit (protein) Preprotein translocase secY subunit (protein) SecBeta (protein)

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1RHZ \| pdb_00001rhz	Download File View File

The structure of a protein conducting channel

van den Berg, B., Clemons Jr., W.M., Collinson, I., Modis, Y., Hartmann, E., Harrison, S.C., Rapoport, T.A.

(2004) Nature 427: 36-44

Released	2004-01-06
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Preprotein translocase secE subunit (protein) Preprotein translocase secY subunit (protein) SecBeta (protein)

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2AKH \| pdb_00002akh	Download File View File

Normal mode-based flexible fitted coordinates of a non-translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli

Mitra, K.M., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks III, C.L., Ban, N., Frank, J.

(2005) Nature 438: 318-324

Released	2005-11-15
Method	ELECTRON MICROSCOPY 14.9 Å
Organisms	Escherichia coli
Macromolecule	Preprotein translocase secE subunit (protein) Preprotein translocase secY subunit (protein) Protein-export membrane protein secG (protein)

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2AKI \| pdb_00002aki	Download File View File

Normal mode-based flexible fitted coordinates of a translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli

Mitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks III, C.L., Ban, N., Frank, J.

(2005) Nature 438: 318-324

Released	2005-11-15
Method	ELECTRON MICROSCOPY 14.9 Å
Organisms	Escherichia coli
Macromolecule	Preprotein translocase secE subunit (protein) Preprotein translocase secY subunit (protein) Protein-export membrane protein secG (protein)

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2YXQ \| pdb_00002yxq	Download File View File

The plug domain of the SecY protein stablizes the closed state of the translocation channel and maintains a membrane seal

Li, W., Schulman, S.

(2007) Mol Cell 26: 511-521

Released	2007-08-14
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Preprotein translocase secG subunit (protein) Preprotein translocase subunit secE (protein) Preprotein translocase subunit secY (protein)

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2YXR \| pdb_00002yxr	Download File View File

The plug domain of the SecY protein stablizes the closed state of the translocation channel and maintains a membrane seal

Li, W., Schulman, S.

(2007) Mol Cell 26: 511-521

Released	2007-08-14
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Preprotein translocase secG subunit (protein) Preprotein translocase subunit secE (protein) Preprotein translocase subunit secY (protein)

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3C0W \| pdb_00003c0w	Download File View File

I-SceI in complex with a bottom nicked DNA substrate

Moure, C.M., Gimble, F.S., Quiocho, F.A.

(2008) Nucleic Acids Res 36: 3287-3296

Released	2008-05-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Intron-encoded endonuclease I-SceI (protein) DNA (5'-D(DAPDCPDGPDCPDTPDAPDGPDGPDGPDAPDTPDAPDAPDCPDAPDGPDGPDGPDTPDAPDAPDTPDAPDC)-3') (nucleic acid) DNA (5'-D(DGPDTPDAPDTPDTPDAPDCPDCPDCPDTPDGPDTPDTPDAPDT)-3') (nucleic acid) DNA (5'-D(PDCPDCPDCPDTPDAPDGPDCPDGPDT)-3') (nucleic acid)
Unique Ligands	CA, NA

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3C0X \| pdb_00003c0x	Download File View File

I-SceI in complex with a top nicked DNA substrate

Moure, C.M., Gimble, F.S., Quiocho, F.A.

(2008) Nucleic Acids Res 36: 3287-3296

Released	2008-05-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Intron-encoded endonuclease I-SceI (protein) DNA (5'-D(DCDAPDCPDGPDCPDTPDAPDGPDGPDGPDAPDTPDAPDA)-3') (nucleic acid) DNA (5'-D(DGDGPDTPDAPDTPDTPDAPDCPDCPDCPDTPDGPDTPDTPDAPDTPDCPDCPDCPDTPDAPDGPDCPDGPDT)-3') (nucleic acid) DNA (5'-D(PDCPDAPDGPDGPDGPDTPDAPDAPDTPDAPDC)-3') (nucleic acid)
Unique Ligands	CA

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3DIN \| pdb_00003din	Download File View File

Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase

Zimmer, J., Nam, Y., Rapoport, T.A.

(2008) Nature 455: 936-943

Released	2008-10-07
Method	X-RAY DIFFRACTION 4.5 Å
Organisms	Thermotoga maritima MSB8 Thermotoga sp. RQ2
Macromolecule	Preprotein translocase subunit SecG (protein) Preprotein translocase subunit SecY (protein) Preprotein translocase subunit secE (protein) Protein translocase subunit secA (protein)
Unique Ligands	ADP, BEF, MG

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3DL8 \| pdb_00003dl8	Download File View File

Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA

Nam, Y., Zimmer, J., Rapoport, T.A.

(2008) Nature 455: 936-943

Released	2008-12-02
Method	X-RAY DIFFRACTION 7.5 Å
Organisms	Aquifex aeolicus Bacillus subtilis
Macromolecule	Preprotein translocase subunit secY (protein) Protein translocase subunit secA (protein) Protein-export membrane protein secG (protein) SecE (protein)

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3J45 \| pdb_00003j45	Download File View File

Structure of a non-translocating SecY protein channel with the 70S ribosome

Menetret, J.F., Park, E., Gumbart, J.C., Ludtke, S.J., Li, W., Whynot, A., Rapoport, T.A., Akey, C.W.

(2013) Nature 506: 102-106

Released	2013-10-23
Method	ELECTRON MICROSCOPY 9.5 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 5

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3MP7 \| pdb_00003mp7	Download File View File

Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes

Egea, P.F., Stroud, R.M., Center for Structures of Membrane Proteins (CSMP)

(2010) Proc Natl Acad Sci U S A 107: 17182-17187

Released	2010-10-06
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Pyrococcus furiosus
Macromolecule	Preprotein translocase subunit secE (protein) Preprotein translocase subunit secY (protein)

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5A0M \| pdb_00005a0m	Download File View File

THE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF MN

Prieto, J., Redondo, P., Merino, N., Villate, M., Blanco, F.J., Molina, R.

(2016) Acta Crystallogr F Struct Biol Commun 72: 473

Released	2016-05-04
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharomyces cerevisiae synthetic construct
Macromolecule	Unique protein chains: 2 Unique nucleic acid chains: 4
Unique Ligands	MN

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5AWW \| pdb_00005aww	Download File View File

Precise Resting State of Thermus thermophilus SecYEG

Tanaka, Y., Sugano, Y., Takemoto, M., Kusakizako, T., Kumazaki, K., Ishitani, R., Nureki, O., Tsukazaki, T.

(2015) Cell Rep 13: 1561-1568

Released	2015-11-25
Method	X-RAY DIFFRACTION 2.724 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein) Putative preprotein translocase, SecG subunit (protein)
Unique Ligands	OLC

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5CH4 \| pdb_00005ch4	Download File View File

Peptide-Bound State of Thermus thermophilus SecYEG

Tanaka, Y., Sugano, Y., Takemoto, M., Kusakizako, T., Kumazaki, K., Ishitani, R., Nureki, O., Tsukazaki, T.

(2015) Cell Rep 13: 1561-1568

Released	2015-11-25
Method	X-RAY DIFFRACTION 3.64 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein) Putative preprotein translocase, SecG subunit (protein)

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5EUL \| pdb_00005eul	Download File View File

Structure of the SecA-SecY complex with a translocating polypeptide substrate

Li, L., Park, E., Ling, J., Ingram, J., Ploegh, H., Rapoport, T.A.

(2016) Nature 531: 395-399

Released	2016-03-09
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 Geobacillus thermodenitrificans NG80-2 Vicugna pacos synthetic construct
Macromolecule	AYC08 (protein) Preprotein translocase SecE subunit (protein) Protein translocase subunit SecA, Insertion Peptide Chimera (protein) Protein translocase subunit SecY (protein)
Unique Ligands	ADP, BEF, MG, TBR

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5MG3 \| pdb_00005mg3	Download File View File

EM fitted model of bacterial holo-translocon

Schaffitzel, C., Botte, M.

(2016) Sci Rep 6: 38399-38399

Released	2016-12-28
Method	ELECTRON MICROSCOPY 14 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 6

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5NCO \| pdb_00005nco	Download File View File

Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome

Jomaa, A., Hwang Fu, Y., Boerhinger, D., Leibundgut, M., Shan, S.O., Ban, N.

(2017) Nat Commun 8: 15470-15470

Released	2017-05-24
Method	ELECTRON MICROSCOPY 4.8 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 36 Unique nucleic acid chains: 4
Unique Ligands	ALF, GDP, MG, ZN

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6ITC \| pdb_00006itc	Download File View File

Structure of a substrate engaged SecA-SecY protein translocation machine

Ma, C.Y., Wu, X.F., Sun, D.J., Park, E.Y., Rapoport, T.A., Gao, N., Long, L.

(2019) Nat Commun 10: 2872-2872

Released	2019-06-12
Method	ELECTRON MICROSCOPY 3.45 Å
Organisms	Aequorea victoria Bacillus subtilis subsp. subtilis str. 168 Escherichia coli Geobacillus thermodenitrificans NG80-2 Lama glama
Macromolecule	Unique protein chains: 7
Unique Ligands	ADP, BEF, MG, PGV

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7XHA \| pdb_00007xha	Download File View File

Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-.

Dong, L., Li, L.

(2023) Proc Natl Acad Sci U S A 120: e2208070120-e2208070120

Released	2023-01-11
Method	ELECTRON MICROSCOPY 3.35 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 Escherichia coli Geobacillus thermodenitrificans NG80-2
Macromolecule	Protein translocase subunit SecA (protein) Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein) Translocating polypeptide (protein)
Unique Ligands	ADP, BEF, MG

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7XHB \| pdb_00007xhb	Download File View File

Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP

Dong, L., Li, L.

(2023) Proc Natl Acad Sci U S A 120: e2208070120-e2208070120

Released	2023-01-11
Method	ELECTRON MICROSCOPY 3.33 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 Escherichia coli Geobacillus thermodenitrificans NG80-2
Macromolecule	Protein translocase subunit SecA (protein) Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein) Translocating peptide (protein)
Unique Ligands	ADP, MG

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8Y9Y \| pdb_00008y9y	Download File View File

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)

Ou, X., Ma, C., Sun, D., Xu, J., Wu, X., Gao, N., Li, L.

(2025) Cell 188: 1912-1924.e13

Released	2025-02-26
Method	ELECTRON MICROSCOPY 3.29 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 Escherichia coli K-12 Geobacillus thermodenitrificans NG80-2
Macromolecule	Protein translocase subunit SecA (protein) Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein) Substrate FtsQ-LacY(+1C) (protein)
Unique Ligands	ADP, BEF, MG

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8Y9Z \| pdb_00008y9z	Download File View File

Structure of the SecA-SecY complex with the substrate HmBRI-3TM

Ou, X., Ma, C., Sun, D., Xu, J., Wu, X., Gao, N., Li, L.

(2025) Cell 188: 1912-1924.e13

Released	2025-02-26
Method	ELECTRON MICROSCOPY 3.41 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 Geobacillus thermodenitrificans NG80-2 Haloarcula marismortui ATCC 43049 Lama glama
Macromolecule	Bacteriorhodopsin-I (protein) Nanobody (protein) Protein translocase subunit SecA (protein) Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein)
Unique Ligands	ADP, BEF, MG

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8YA0 \| pdb_00008ya0	Download File View File

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C)

Ou, X., Ma, C., Sun, D., Xu, J., Wu, X., Gao, N., Li, L.

(2025) Cell 188: 1912-1924.e13

Released	2025-02-26
Method	ELECTRON MICROSCOPY 2.97 Å
Organisms	Aequorea victoria Bacillus subtilis subsp. subtilis str. 168 Escherichia coli K-12 Geobacillus thermodenitrificans NG80-2 Lama glama
Macromolecule	Unique protein chains: 7
Unique Ligands	ADP, BEF, MG

1 to 25 of 28 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1R7M | pdb_00001r7m

1RH5 | pdb_00001rh5

1RHZ | pdb_00001rhz

2AKH | pdb_00002akh

2AKI | pdb_00002aki

2YXQ | pdb_00002yxq

2YXR | pdb_00002yxr

3C0W | pdb_00003c0w

3C0X | pdb_00003c0x

3DIN | pdb_00003din

3DL8 | pdb_00003dl8

3J45 | pdb_00003j45

3MP7 | pdb_00003mp7

5A0M | pdb_00005a0m

5AWW | pdb_00005aww

5CH4 | pdb_00005ch4

5EUL | pdb_00005eul

5MG3 | pdb_00005mg3

5NCO | pdb_00005nco

6ITC | pdb_00006itc

7XHA | pdb_00007xha

7XHB | pdb_00007xhb

8Y9Y | pdb_00008y9y

8Y9Z | pdb_00008y9z

8YA0 | pdb_00008ya0