› 5cci

X-ray diffraction
4.1Å resolution

Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form)

Released:
DOI: 10.2210/pdb5cci/pdb
PDB entry 5cci coloured by chain, front view.
PDB entry 5cci coloured by chain, side view.
PDB entry 5cci coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis.
Zhou Q, Lai Y, Bacaj T, Zhao M, Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Sauter NK, Cohen AE, Soltis SM, Alonso-Mori R, Chollet M, Lemke HT, Pfuetzner RA, Choi UB, Weis WI, Diao J, Südhof TC, Brunger AT
Nature 525 62-7 (2015)
PMID: 26280336

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
PDBe Complex ID:
PDB-CPX-149385 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Vesicle-associated membrane protein 2 Chain: A
Molecule details ›
Chain: A
Length: 63 amino acids
Theoretical weight: 7.23 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63045 (Residues: 28-89; Coverage: 53%)
Gene names: Syb2, Vamp2
Sequence domains: Synaptobrevin
Syntaxin-1A Chain: B
Molecule details ›
Chain: B
Length: 67 amino acids
Theoretical weight: 7.84 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32851 (Residues: 190-256; Coverage: 23%)
Gene names: Sap, Stx1a
Sequence domains: SNARE domain
Synaptosomal-associated protein 25 Chain: C
Molecule details ›
Chain: C
Length: 77 amino acids
Theoretical weight: 9.03 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P60881 (Residues: 7-83; Coverage: 37%)
Gene names: Snap, Snap25
Synaptosomal-associated protein 25 Chain: D
Molecule details ›
Chain: D
Length: 65 amino acids
Theoretical weight: 7.47 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P60881 (Residues: 141-204; Coverage: 31%)
Gene names: Snap, Snap25
Synaptotagmin-1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 281 amino acids
Theoretical weight: 32.25 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21707 (Residues: 141-421; Coverage: 67%)
Gene name: Syt1
Sequence domains: C2 domain

Ligands and Environments

1 bound ligand:
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21212
Unit cell:
a: 69.064Å b: 171.759Å c: 146.561Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.279 0.276 0.323
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

39 review citations

The Mechanisms and Functions of Synaptic Facilitation.
Jackman et al. (2017)
38 more

8 mentions without citation

Molecular Mechanisms of Fast Neurotransmitter Release.
Brunger et al. (2018)
7 more