PDBe 5kj8

X-ray diffraction
4.1Å resolution

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

Released:

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
monomeric
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
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
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
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%)
  • Best match: P60881-2 (Residues: 9-83)
Gene names: Snap, Snap25
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
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

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 68.79Å b: 169.71Å c: 286.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.284 0.283 0.297
Expression system: Escherichia coli