7KAU

Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3 double mutant, class with Sec62


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1038/s41594-020-00541-x
  • Primary Citation of Related Structures:  
    7KAH, 7KAK, 7KAL, 7KAI, 7KAJ, 7KAU, 7KAO, 7KAP, 7KAM, 7KAN

  • 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 ...

    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

    California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA. eunyong_park@berkeley.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein SEC61A480Saccharomyces cerevisiae BY4741Mutation(s): 4 
Membrane Entity: Yes 
UniProt
Find proteins for P32915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32915
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence 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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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence 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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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocation protein SEC63D676Saccharomyces cerevisiae BY4741Mutation(s): 0 
Gene Names: SEC63NPL1PTL1YOR254C
Membrane Entity: Yes 
UniProt
Find proteins for P14906 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P14906
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Translocation protein SEC66E206Saccharomyces cerevisiae BY4741Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P33754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Translocation protein SEC72F193Saccharomyces 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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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec62G56Saccharomyces cerevisiae BY4741Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-10-01 
  • Released Date: 2021-01-06 
  • Deposition Author(s): Itskanov, S., Park, E.

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