5W5D

Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/nature23484
  • Primary Citation of Related Structures:  
    5W5C, 5W5D

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-associated membrane protein 240Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
UniProt
Find proteins for P63045 (Rattus norvegicus)
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UniProt GroupP63045
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Syntaxin-1A67Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
UniProt
Find proteins for P32851 (Rattus norvegicus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 2577Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
UniProt
Find proteins for P60881 (Rattus norvegicus)
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UniProt GroupP60881
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 2565Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
UniProt
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UniProt GroupP60881
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Complexin-183Rattus norvegicusMutation(s): 0 
Gene Names: Cplx1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin-1152Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
UniProt
Find proteins for P21707 (Rattus norvegicus)
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UniProt GroupP21707
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.202α = 90
b = 89.199β = 90
c = 87.202γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description