5CCH

Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis.

Zhou, Q.Lai, Y.Bacaj, T.Zhao, M.Lyubimov, A.Y.Uervirojnangkoorn, M.Zeldin, O.B.Brewster, A.S.Sauter, N.K.Cohen, A.E.Soltis, S.M.Alonso-Mori, R.Chollet, M.Lemke, H.T.Pfuetzner, R.A.Choi, U.B.Weis, W.I.Diao, J.Sudhof, T.C.Brunger, A.T.

(2015) Nature 525: 62-67

  • DOI: https://doi.org/10.1038/nature14975
  • Primary Citation of Related Structures:  
    5CCG, 5CCH, 5CCI, 5CCJ

  • PubMed Abstract: 

    Synaptotagmin-1 and neuronal SNARE proteins have central roles in evoked synchronous neurotransmitter release; however, it is unknown how they cooperate to trigger synaptic vesicle fusion. Here we report atomic-resolution crystal structures of Ca(2+)- and Mg(2+)-bound complexes between synaptotagmin-1 and the neuronal SNARE complex, one of which was determined with diffraction data from an X-ray free-electron laser, leading to an atomic-resolution structure with accurate rotamer assignments for many side chains. The structures reveal several interfaces, including a large, specific, Ca(2+)-independent and conserved interface. Tests of this interface by mutagenesis suggest that it is essential for Ca(2+)-triggered neurotransmitter release in mouse hippocampal neuronal synapses and for Ca(2+)-triggered vesicle fusion in a reconstituted system. We propose that this interface forms before Ca(2+) triggering, moves en bloc as Ca(2+) influx promotes the interactions between synaptotagmin-1 and the plasma membrane, and consequently remodels the membrane to promote fusion, possibly in conjunction with other interfaces.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-associated membrane protein 263Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
UniProt
Find proteins for P63045 (Rattus norvegicus)
Explore P63045 
Go to UniProtKB:  P63045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63045
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Syntaxin-1A67Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
UniProt
Find proteins for P32851 (Rattus norvegicus)
Explore P32851 
Go to UniProtKB:  P32851
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32851
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 2577Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
UniProt
Find proteins for P60881 (Rattus norvegicus)
Explore P60881 
Go to UniProtKB:  P60881
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60881
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 2565Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
UniProt
Find proteins for P60881 (Rattus norvegicus)
Explore P60881 
Go to UniProtKB:  P60881
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60881
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin-1
E, F
281Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
UniProt
Find proteins for P21707 (Rattus norvegicus)
Explore P21707 
Go to UniProtKB:  P21707
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21707
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.073α = 90
b = 171.626β = 90
c = 146.942γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2015-09-09
    Changes: Derived calculations
  • Version 1.3: 2015-09-16
    Changes: Database references
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description