5CCG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.323 

wwPDB Validation   3D Report Full Report


This is version 1.6 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-associated membrane protein 2
A, G
63Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
Membrane Entity: Yes 
UniProt
Find proteins for P63045 (Rattus norvegicus)
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UniProt GroupP63045
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Syntaxin-1A
B, H
67Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
Membrane Entity: Yes 
UniProt
Find proteins for P32851 (Rattus norvegicus)
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UniProt GroupP32851
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 25
C, I
77Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Membrane Entity: Yes 
UniProt
Find proteins for P60881 (Rattus norvegicus)
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UniProt GroupP60881
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 25
D, J
65Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Membrane Entity: Yes 
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Find proteins for P60881 (Rattus norvegicus)
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UniProt GroupP60881
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin-1
E, F, K
281Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Membrane Entity: Yes 
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
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth K]
BA [auth K]
CA [auth K]
DA [auth K]
L [auth A]
AA [auth K],
BA [auth K],
CA [auth K],
DA [auth K],
L [auth A],
M [auth A],
N [auth C],
O [auth C],
P [auth C],
Q [auth D],
R [auth E],
S [auth E],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth F],
Y [auth F],
Z [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.323 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.603α = 90
b = 171.092β = 90
c = 291.879γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
PHASERphasing

Structure Validation

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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: Data collection, Database references
  • Version 1.2: 2015-09-09
    Changes: Derived calculations
  • Version 1.3: 2015-09-16
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2018-02-14
    Changes: Data collection
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description