7KAT

Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3 double mutant, class without Sec62


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62.

Itskanov, S.Kuo, K.M.Gumbart, J.C.Park, E.

(2021) Nat Struct Mol Biol 28: 162-172

  • DOI: https://doi.org/10.1038/s41594-020-00541-x
  • Primary Citation of Related Structures:  
    7KAH, 7KAI, 7KAJ, 7KAK, 7KAL, 7KAM, 7KAN, 7KAO, 7KAP, 7KAQ, 7KAR, 7KAS, 7KAT, 7KAU, 7KB5

  • PubMed Abstract: 

    Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. In the present study, we determined cryo-electron microscopy (cryo-EM) structures of several variants of Sec61-Sec62-Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and luminal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational protein translocation.


  • Organizational Affiliation

    Biophysics Graduate Program, University of California, Berkeley, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC61480Saccharomyces cerevisiae BY4741Mutation(s): 4 
Membrane Entity: Yes 
UniProt
Find proteins for P32915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32915 
Go to UniProtKB:  P32915
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UniProt GroupP32915
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SSS1B [auth C]80Saccharomyces cerevisiae BY4741Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P35179 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P35179
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UniProt GroupP35179
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SBH1C [auth B]82Saccharomyces cerevisiae BY4741Mutation(s): 0 
Gene Names: SBH1SEB1YER087C-BYER087BC
Membrane Entity: Yes 
UniProt
Find proteins for P52870 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P52870
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UniProt GroupP52870
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocation protein SEC63676Saccharomyces cerevisiae BY4741Mutation(s): 2 
Gene Names: SEC63NPL1PTL1YOR254C
Membrane Entity: Yes 
UniProt
Find proteins for P14906 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14906 
Go to UniProtKB:  P14906
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UniProt GroupP14906
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translocation protein SEC66206Saccharomyces cerevisiae BY4741Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P33754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P33754
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UniProt GroupP33754
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Translocation protein SEC72193Saccharomyces cerevisiae BY4741Mutation(s): 0 
UniProt
Find proteins for P39742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39742 
Go to UniProtKB:  P39742
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UniProt GroupP39742
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.12

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references