2N1T | pdb_00002n1t

Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 
  • Selection Criteria: Contribution to fit PCS data 

wwPDB Validation 3D Report Full Report

Validation slider image for 2N1T

This is version 1.4 of the entry. See complete history

Literature

Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution.

Brewer, K.D.Bacaj, T.Cavalli, A.Camilloni, C.Swarbrick, J.D.Liu, J.Zhou, A.Zhou, P.Barlow, N.Xu, J.Seven, A.B.Prinslow, E.A.Voleti, R.Haussinger, D.Bonvin, A.M.Tomchick, D.R.Vendruscolo, M.Graham, B.Sudhof, T.C.Rizo, J.

(2015) Nat Struct Mol Biol 22: 555-564

  • DOI: https://doi.org/10.1038/nsmb.3035
  • Primary Citation Related Structures: 
    2N1T

  • PubMed Abstract: 

    Rapid neurotransmitter release depends on the Ca2+ sensor Synaptotagmin-1 (Syt1) and the SNARE complex formed by synaptobrevin, syntaxin-1 and SNAP-25. How Syt1 triggers release has been unclear, partly because elucidating high-resolution structures of Syt1-SNARE complexes has been challenging. An NMR approach based on lanthanide-induced pseudocontact shifts now reveals a dynamic binding mode in which basic residues in the concave side of the Syt1 C2B-domain β-sandwich interact with a polyacidic region of the SNARE complex formed by syntaxin-1 and SNAP-25. The physiological relevance of this dynamic structural model is supported by mutations in basic residues of Syt1 that markedly impair SNARE-complex binding in vitro and Syt1 function in neurons. Mutations with milder effects on binding have correspondingly milder effects on Syt1 function. Our results support a model whereby dynamic interaction facilitates cooperation between Syt1 and the SNAREs in inducing membrane fusion.


  • Organizational Affiliation
    • 1] Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA. [2] Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA. [3] Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Macromolecule Content 

  • Total Structure Weight: 51.43 kDa 
  • Atom Count: 3,591 
  • Modeled Residue Count: 448 
  • Deposited Residue Count: 448 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vesicle-associated membrane protein 269Rattus norvegicusMutation(s): 0 
Gene Names: Syb2Vamp2
Membrane Entity: Yes 
UniProt
Find proteins for P63045 (Rattus norvegicus)
Explore P63045 
Go to UniProtKB:  P63045
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UniProt GroupP63045
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Syntaxin-1A72Rattus norvegicusMutation(s): 0 
Gene Names: SapStx1a
Membrane Entity: Yes 
UniProt
Find proteins for P32851 (Rattus norvegicus)
Explore P32851 
Go to UniProtKB:  P32851
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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 2577Homo sapiensMutation(s): 0 
Gene Names: SNAPSNAP25SNAP-25A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P60880 (Homo sapiens)
Explore P60880 
Go to UniProtKB:  P60880
PHAROS:  P60880
GTEx:  ENSG00000132639 
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UniProt GroupP60880
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 2574Homo sapiensMutation(s): 0 
Gene Names: SNAPSNAP25SNAP-25A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P60880 (Homo sapiens)
Explore P60880 
Go to UniProtKB:  P60880
PHAROS:  P60880
GTEx:  ENSG00000132639 
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UniProt GroupP60880
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Synaptotagmin-1156Homo sapiensMutation(s): 0 
Gene Names: SVP65SYTSYT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens)
Explore P21579 
Go to UniProtKB:  P21579
PHAROS:  P21579
GTEx:  ENSG00000067715 
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UniProt GroupP21579
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 
  • Selection Criteria: Contribution to fit PCS data 

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2021-08-18
    Changes: Data collection, Database references, Experimental preparation, Refinement description
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references