8YA0 | pdb_00008ya0

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

SecY translocon chaperones protein folding during membrane protein insertion.

Ou, X.Ma, C.Sun, D.Xu, J.Wang, Y.Wu, X.Wang, D.Yang, S.Gao, N.Song, C.Li, L.

(2025) Cell 188: 1912-1924.e13

  • DOI: https://doi.org/10.1016/j.cell.2025.01.037
  • Primary Citation of Related Structures:  
    8Y9Y, 8Y9Z, 8YA0, 8YA2, 8YA3, 8YAS

  • PubMed Abstract: 

    The Sec translocon is vital for guiding membrane protein insertion into lipid bilayers. The insertion and folding processes of membrane proteins are poorly understood. Here, we report cryo-electron microscopy structures of multi-spanning membrane proteins inserting through the SecY channel, the Sec translocon in prokaryotes. The high-resolution structures illustrate how bulky amino acids pass the narrow channel restriction. Comparison of different translocation states reveals that the cytoplasmic and extracellular cavities of the channel create distinct environments for promoting the unfolding and folding of transmembrane segments (TMs), respectively. Released substrate TMs are either flexible or stabilized by an unexpected hydrophilic groove between TM3 and TM4 of SecY. Disruption of the groove causes global defects in the folding of the membrane proteome. These findings demonstrate that beyond its role as a passive protein-conducting channel, the SecY translocon actively serves as a chaperone, employing multiple mechanisms to promote membrane protein insertion and folding.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecA765Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: secA
EC: 7.4.2.8
Membrane Entity: Yes 
UniProt
Find proteins for P28366 (Bacillus subtilis (strain 168))
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UniProt GroupP28366
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecYB [auth Y]429Geobacillus thermodenitrificans NG80-2Mutation(s): 4 
Gene Names: secY
Membrane Entity: Yes 
UniProt
Find proteins for A4IJK8 (Geobacillus thermodenitrificans (strain NG80-2))
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UniProt GroupA4IJK8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecEC [auth E]58Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Gene Names: secE
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NanobodyD [auth V]116Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein FtsQ,Lactose permeaseE [auth B]72Escherichia coli K-12Mutation(s): 6 
Gene Names: ftsQlacY
Membrane Entity: Yes 
UniProt
Find proteins for P02920 (Escherichia coli (strain K12))
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Find proteins for Q7CR81 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NanobodyF [auth C]113Lama glamaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein225Aequorea victoriaMutation(s): 5 
Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2019YFA0508900,2016YFA0500401
National Natural Science Foundation of China (NSFC)China31725007,31630087,31800625,21873006,31870835
Other government2018M631249,2019M650327

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-16
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-18
    Changes: Data collection