7AFT

Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • 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

Architecture of the active post-translational Sec translocon.

Weng, T.H.Steinchen, W.Beatrix, B.Berninghausen, O.Becker, T.Bange, G.Cheng, J.Beckmann, R.

(2021) EMBO J 40: e105643-e105643

  • DOI: https://doi.org/10.15252/embj.2020105643
  • Primary Citation of Related Structures:  
    6ZZZ, 7AFT

  • PubMed Abstract: 

    In eukaryotes, most secretory and membrane proteins are targeted by an N-terminal signal sequence to the endoplasmic reticulum, where the trimeric Sec61 complex serves as protein-conducting channel (PCC). In the post-translational mode, fully synthesized proteins are recognized by a specialized channel additionally containing the Sec62, Sec63, Sec71, and Sec72 subunits. Recent structures of this Sec complex in the idle state revealed the overall architecture in a pre-opened state. Here, we present a cryo-EM structure of the yeast Sec complex bound to a substrate, and a crystal structure of the Sec62 cytosolic domain. The signal sequence is inserted into the lateral gate of Sec61α similar to previous structures, yet, with the gate adopting an even more open conformation. The signal sequence is flanked by two Sec62 transmembrane helices, the cytoplasmic N-terminal domain of Sec62 is more rigidly positioned, and the plug domain is relocated. We crystallized the Sec62 domain and mapped its interaction with the C-terminus of Sec63. Together, we obtained a near-complete and integrated model of the active Sec complex.


  • Organizational Affiliation

    Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC61480Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32915 
Go to UniProtKB:  P32915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32915
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SBH182Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P52870 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52870 
Go to UniProtKB:  P52870
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52870
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SSS180Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P35179 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35179 
Go to UniProtKB:  P35179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35179
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocation protein SEC63663Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14906 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14906 
Go to UniProtKB:  P14906
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14906
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translocation protein SEC66206Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P33754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33754 
Go to UniProtKB:  P33754
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33754
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Translocation protein SEC72193Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39742 
Go to UniProtKB:  P39742
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39742
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Translocation protein SEC62,Translocation protein SEC62324Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEC62YPL094CLPG14C
Membrane Entity: Yes 
UniProt
Find proteins for P21825 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21825 
Go to UniProtKB:  P21825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21825
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mating factor alpha-1,Mating factor alpha-1178Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MF(ALPHA)1MF-ALPHA-1MFAL1YPL187W
Membrane Entity: Yes 
UniProt
Find proteins for P01149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P01149 
Go to UniProtKB:  P01149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01149
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-02-10
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description