› 5kj7

X-ray diffraction
3.5Å resolution

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

Released:
DOI: 10.2210/pdb5kj7/pdb
PDB entry 5kj7 coloured by chain, front view.
PDB entry 5kj7 coloured by chain, side view.
PDB entry 5kj7 coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.
Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT
Elife 5 (2016)
PMID: 27731796

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
monomeric
PDBe Complex ID:
PDB-CPX-149381 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Vesicle-associated membrane protein 3 Chains: A, G
Molecule details ›
Chains: A, G
Length: 63 amino acids
Theoretical weight: 7.23 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P63025 (Residues: 14-76; Coverage: 61%)
Gene names: Syb3, Vamp3
Sequence domains: Synaptobrevin
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Syntaxin-1A Chains: B, H
Molecule details ›
Chains: B, H
Length: 66 amino acids
Theoretical weight: 7.71 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P32851 (Residues: 191-256; Coverage: 23%)
Gene names: Sap, Stx1a
Sequence domains: SNARE domain
Synaptosomal-associated protein 25 Chains: C, I
Molecule details ›
Chains: C, I
Length: 75 amino acids
Theoretical weight: 8.74 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P60881 (Residues: 9-83; Coverage: 36%)
Gene names: Snap, Snap25
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Synaptosomal-associated protein 25 Chains: D, J
Molecule details ›
Chains: D, J
Length: 64 amino acids
Theoretical weight: 7.34 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P60881 (Residues: 141-204; Coverage: 31%)
Gene names: Snap, Snap25
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Synaptotagmin-1 Chains: E, F, K
Molecule details ›
Chains: E, F, K
Length: 279 amino acids
Theoretical weight: 31.99 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P21707 (Residues: 141-419; Coverage: 66%)
Gene name: Syt1
Sequence domains: C2 domain
Structure domains: C2 domain

Ligands and Environments

1 bound ligand:
Ligand CA 19 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLAC LCLS BEAMLINE XPP
Spacegroup: P212121
Unit cell:
a: 69.386Å b: 170.676Å c: 291.014Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.294 0.292 0.329
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models.
Wang et al. (2017)
9 other articles

12 mentions without citation

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