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 1.5 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
  • Primary Citation of Related Structures:  
    5CCH, 5CCG, 5CCJ, 5CCI

  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vesicle-associated membrane protein 2A, G63Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
Membrane Entity: Yes 
UniProt
Find proteins for P63045 (Rattus norvegicus)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Syntaxin-1AB, H67Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
Membrane Entity: Yes 
UniProt
Find proteins for P32851 (Rattus norvegicus)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptosomal-associated protein 25C, I77Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Membrane Entity: Yes 
UniProt
Find proteins for P60881 (Rattus norvegicus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptosomal-associated protein 25D, J65Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptotagmin-1E, F, K281Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Membrane Entity: Yes 
UniProt
Find proteins for P21707 (Rattus norvegicus)
Explore P21707 
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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] , M [auth A] , N [auth C] , O [auth C] , 
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
 Ligand Interaction
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