3B5N

Structure of the yeast plasma membrane SNARE complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Structure of the Yeast Plasma Membrane SNARE Complex Reveals Destabilizing Water-filled Cavities.

Strop, P.Kaiser, S.E.Vrljic, M.Brunger, A.T.

(2008) J Biol Chem 283: 1113-1119

  • DOI: https://doi.org/10.1074/jbc.M707912200
  • Primary Citation of Related Structures:  
    3B5N

  • PubMed Abstract: 

    SNARE proteins form a complex that leads to membrane fusion between vesicles, organelles, and plasma membrane in all eukaryotic cells. We report the 1.7A resolution structure of the SNARE complex that mediates exocytosis at the plasma membrane in the yeast Saccharomyces cerevisiae. Similar to its neuronal and endosomal homologues, the S. cerevisiae SNARE complex forms a parallel four-helix bundle in the center of which is an ionic layer. The S. cerevisiae SNARE complex exhibits increased helix bending near the ionic layer, contains water-filled cavities in the complex core, and exhibits reduced thermal stability relative to mammalian SNARE complexes. Mutagenesis experiments suggest that the water-filled cavities contribute to the lower stability of the S. cerevisiae complex.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptobrevin homolog 1
A, E, I
61Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SNC1
UniProt
Find proteins for P31109 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P31109
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UniProt GroupP31109
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SSO1
B, F, J
69Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SSO1
UniProt
Find proteins for P32867 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32867
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UniProt GroupP32867
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC9
C, G, K
70Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEC9HSS7
UniProt
Find proteins for P40357 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P40357
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UniProt GroupP40357
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC9
D, H, L
64Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEC9HSS7
UniProt
Find proteins for P40357 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40357 
Go to UniProtKB:  P40357
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40357
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.956α = 90
b = 48.113β = 97.77
c = 110.265γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description