6ND1

CryoEM structure of the Sec Complex from yeast


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the post-translational protein translocation machinery of the ER membrane.

Wu, X.Cabanos, C.Rapoport, T.A.

(2019) Nature 566: 136-139

  • DOI: https://doi.org/10.1038/s41586-018-0856-x
  • Primary Citation of Related Structures:  
    6ND1

  • PubMed Abstract: 

    Many proteins must translocate through the protein-conducting Sec61 channel in the eukaryotic endoplasmic reticulum membrane or the SecY channel in the prokaryotic plasma membrane 1,2 . Proteins with highly hydrophobic signal sequences are first recognized by the signal recognition particle (SRP) 3,4 and then moved co-translationally through the Sec61 or SecY channel by the associated translating ribosome. Substrates with less hydrophobic signal sequences bypass the SRP and are moved through the channel post-translationally 5,6 . In eukaryotic cells, post-translational translocation is mediated by the association of the Sec61 channel with another membrane protein complex, the Sec62-Sec63 complex 7-9 , and substrates are moved through the channel by the luminal BiP ATPase 9 . How the Sec62-Sec63 complex activates the Sec61 channel for post-translational translocation is not known. Here we report the electron cryo-microscopy structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins. Sec63 causes wide opening of the lateral gate of the Sec61 channel, priming it for the passage of low-hydrophobicity signal sequences into the lipid phase, without displacing the channel's plug domain. Lateral channel opening is triggered by Sec63 interacting both with cytosolic loops in the C-terminal half of Sec61 and transmembrane segments in the N-terminal half of the Sec61 channel. The cytosolic Brl domain of Sec63 blocks ribosome binding to the channel and recruits Sec71 and Sec72, positioning them for the capture of polypeptides associated with cytosolic Hsp70 10 . Our structure shows how the Sec61 channel is activated for post-translational protein translocation.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC61A [auth B]480Saccharomyces cerevisiaeMutation(s): 0 
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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UniProt GroupP32915
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocation protein SEC63B [auth A]677Saccharomyces cerevisiaeMutation(s): 0 
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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UniProt GroupP14906
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SSS180Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P35179 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP35179
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SBH182Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P52870 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP52870
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translocation protein SEC66206Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P33754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Translocation protein SEC72193Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P39742
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UniProt GroupP39742
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM052586

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references