1GL2 | pdb_00001gl2

Crystal structure of an endosomal SNARE core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.224 (Depositor) 
  • R-Value Work: 
    0.176 (Depositor) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Crystal Structure of the Endosomal Snare Complex Reveals Common Structural Principles of All Snares.

Antonin, W.Fasshauer, D.Becker, S.Jahn, R.Schneider, T.R.

(2001) Nat Struct Biol 9: 107

  • DOI: https://doi.org/10.1038/nsb746
  • Primary Citation Related Structures: 
    1GL2

  • PubMed Abstract: 

    SNARE proteins are crucial for intracellular membrane fusion in all eukaryotes. These proteins assemble into tight complexes that connect membranes and may induce fusion. The crystal structure of the neuronal core complex is represented by an unusually long bundle of four alpha-helices connected by 16 layers of mostly hydrophobic amino acids. Here we report the 1.9 A resolution crystal structure of an endosomal SNARE core complex containing four SNAREs: syntaxin 7, syntaxin 8, vti1b and endobrevin/VAMP-8. Despite limited sequence homology, the helix alignment and the layer structure of the endosomal complex are remarkably similar to those of the neuronal complex. However, subtle variations are evident that characterize different SNARE subfamilies. We conclude that the structure of the SNARE core complex is an evolutionarily conserved hallmark of all SNARE complexes and is intimately associated with the general role of SNAREs in membrane fusion.


  • Organizational Affiliation
    • Department of Neurobiology and Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 29.58 kDa 
  • Atom Count: 2,026 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 260 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ENDOBREVIN65Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q9WUF4 (Rattus norvegicus)
Explore Q9WUF4 
Go to UniProtKB:  Q9WUF4
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UniProt GroupQ9WUF4
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SYNTAXIN 765Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O70439 (Mus musculus)
Explore O70439 
Go to UniProtKB:  O70439
IMPC:  MGI:1858210
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UniProt GroupO70439
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 165Mus musculusMutation(s): 0 
UniProt
Find proteins for O88384 (Mus musculus)
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Go to UniProtKB:  O88384
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UniProt GroupO88384
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SYNTAXIN 865Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q9Z2Q7 (Rattus norvegicus)
Explore Q9Z2Q7 
Go to UniProtKB:  Q9Z2Q7
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UniProt GroupQ9Z2Q7
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.224 (Depositor) 
  • R-Value Work:  0.176 (Depositor) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.7α = 90
b = 41.1β = 109.4
c = 51.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-05-30
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 2.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description