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 1.3 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: 10.1038/nature14975
  • Structures With Same Primary Citation

  • 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+) ...

    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

    Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vesicle-associated membrane protein 2
A
63Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
Find proteins for P63045 (Rattus norvegicus)
Go to UniProtKB:  P63045

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Syntaxin-1A
B
67Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
Find proteins for P32851 (Rattus norvegicus)
Go to UniProtKB:  P32851

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 25
C
77Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Find proteins for P60881 (Rattus norvegicus)
Go to UniProtKB:  P60881

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 25
D
65Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Find proteins for P60881 (Rattus norvegicus)
Go to UniProtKB:  P60881

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Synaptotagmin-1
E, F
281Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Find proteins for P21707 (Rattus norvegicus)
Go to UniProtKB:  P21707
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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