5W5C

Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The primed SNARE-complexin-synaptotagmin complex for neuronal exocytosis.

Zhou, Q.Zhou, P.Wang, A.L.Wu, D.Zhao, M.Sudhof, T.C.Brunger, A.T.

(2017) Nature 548: 420-425

  • DOI: 10.1038/nature23484
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Synaptotagmin, complexin, and neuronal SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins mediate evoked synchronous neurotransmitter release, but the molecular mechanisms mediating the cooperation between these mo ...

    Synaptotagmin, complexin, and neuronal SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins mediate evoked synchronous neurotransmitter release, but the molecular mechanisms mediating the cooperation between these molecules remain unclear. Here we determine crystal structures of the primed pre-fusion SNARE-complexin-synaptotagmin-1 complex. These structures reveal an unexpected tripartite interface between synaptotagmin-1 and both the SNARE complex and complexin. Simultaneously, a second synaptotagmin-1 molecule interacts with the other side of the SNARE complex via the previously identified primary interface. Mutations that disrupt either interface in solution also severely impair evoked synchronous release in neurons, suggesting that both interfaces are essential for the primed pre-fusion state. Ca 2+ binding to the synaptotagmin-1 molecules unlocks the complex, allows full zippering of the SNARE complex, and triggers membrane fusion. The tripartite SNARE-complexin-synaptotagmin-1 complex at a synaptic vesicle docking site has to be unlocked for triggered fusion to start, explaining the cooperation between complexin and synaptotagmin-1 in synchronizing evoked release on the sub-millisecond timescale.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vesicle-associated membrane protein 2
A
40Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
Find proteins for P63045 (Rattus norvegicus)
Go to UniProtKB:  P63045

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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: 5
MoleculeChainsSequence LengthOrganismDetails
Complexin-1
E
83Rattus norvegicusMutation(s): 0 
Gene Names: Cplx1
Find proteins for P63041 (Rattus norvegicus)
Go to UniProtKB:  P63041

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Synaptotagmin-1
F
282Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Find proteins for P21707 (Rattus norvegicus)
Go to UniProtKB:  P21707

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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: 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
D, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.663α = 90
b = 89.683β = 90
c = 91.728γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Database references