› 5w5d

X-ray diffraction
2.5Å resolution

Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex

Released:
DOI: 10.2210/pdb5w5d/pdb
PDB entry 5w5d coloured by chain, front view.
PDB entry 5w5d coloured by chain, side view.
PDB entry 5w5d coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
The primed SNARE-complexin-synaptotagmin complex for neuronal exocytosis.
Zhou Q, Zhou P, Wang AL, Wu D, Zhao M, Südhof TC, Brunger AT
Nature 548 420-425 (2017)
PMID: 28813412

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-149384 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Vesicle-associated membrane protein 2 Chain: A
Molecule details ›
Chain: A
Length: 40 amino acids
Theoretical weight: 4.7 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P63045 (Residues: 28-66; Coverage: 34%)
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
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
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
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
Complexin-1 Chain: E
Molecule details ›
Chain: E
Length: 83 amino acids
Theoretical weight: 9.61 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P63041 (Residues: 1-83; Coverage: 62%)
Gene name: Cplx1
Sequence domains: Synaphin protein
Synaptotagmin-1 Chain: F
Molecule details ›
Chain: F
Length: 152 amino acids
Theoretical weight: 17.35 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P21707 (Residues: 270-421; Coverage: 36%)
Gene name: Syt1
Sequence domains: C2 domain
Structure domains: C2 domain

Ligands and Environments

1 bound ligand:
Ligand MG 1 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: 85.202Å b: 89.199Å c: 87.202Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.231
Expression system: Escherichia coli

Quick links

Citations

40 review citations

Mechanism of neurotransmitter release coming into focus.
Rizo J. (2018)
39 more

7 mentions without citation

The Core Complex of the Ca2+-Triggered Presynaptic Fusion Machinery.
Brunger et al. (2023)
6 more