5M4Y

Crystal structure of the Sec3/Sso2 complex at 2.20 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Sec3 promotes the initial binary t-SNARE complex assembly and membrane fusion.

Yue, P.Zhang, Y.Mei, K.Wang, S.Lesigang, J.Zhu, Y.Dong, G.Guo, W.

(2017) Nat Commun 8: 14236-14236

  • DOI: https://doi.org/10.1038/ncomms14236
  • Primary Citation of Related Structures:  
    5LG4, 5M4Y

  • PubMed Abstract: 

    The soluble N-ethylmaleimide-sensitive factor-attachment protein receptors (SNAREs) constitute the core machinery for membrane fusion during eukaryotic cell vesicular trafficking. However, how the assembly of the SNARE complex is initiated is unknown. Here we report that Sec3, a component of the exocyst complex that mediates vesicle tethering during exocytosis, directly interacts with the t-SNARE protein Sso2. This interaction promotes the formation of an Sso2-Sec9 'binary' t-SNARE complex, the early rate-limiting step in SNARE complex assembly, and stimulates membrane fusion. The crystal structure of the Sec3-Sso2 complex suggests that Sec3 binding induces conformational changes of Sso2 that are crucial for the relief of its auto-inhibition. Interestingly, specific disruption of the Sec3-Sso2 interaction in cells blocks exocytosis without affecting the function of Sec3 in vesicle tethering. Our study reveals an activation mechanism for SNARE complex assembly, and uncovers a role of the exocyst in promoting membrane fusion in addition to vesicle tethering.


  • Organizational Affiliation

    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SSO2
A, C, E
210Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SSO2YMR183CYM8010.13C
UniProt
Find proteins for P39926 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39926 
Go to UniProtKB:  P39926
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39926
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exocyst complex component SEC3
B, D, F
250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEC3PSL1YER008C
UniProt
Find proteins for P33332 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33332 
Go to UniProtKB:  P33332
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33332
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.145α = 90
b = 135.803β = 90
c = 185.738γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP24929-B21

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.0: 2019-10-16
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description