SMTL ID : 5ccg.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-1-3-mer

Ligands

18 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 2 residues within 4Å: Chain A: E.29 Ligands: CA.2 No protein-ligand interaction detected (PLIP) CA.2: 2 residues within 4Å: Chain A: E.36 Ligands: CA.1 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain C: G.48 Chain D: Q.38 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain C: D.52, E.55 Chain D: R.41 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.55, C:E.55 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain E: D.163, D.169, D.223, Y.224, D.225 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.169, E:Y.224, E:D.225 CA.8: 4 residues within 4Å: Chain E: D.32, D.90, F.91, D.92 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.32, E:D.90, E:D.90, E:F.91 CA.9: 3 residues within 4Å: Chain E: D.32, D.38, R.93 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.32 CA.10: 4 residues within 4Å: Chain E: M.162, D.163, D.223, D.225 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.225, E:D.225 CA.11: 5 residues within 4Å: Chain F: D.32, D.38, D.90, F.91, D.92 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.32, F:D.38, F:F.91 CA.12: 3 residues within 4Å: Chain F: D.32, D.90, D.92 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.32, F:D.90, F:D.92, F:D.92 CA.13: 3 residues within 4Å: Chain F: D.163, D.169, Y.224 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.169, F:Y.224 CA.14: 4 residues within 4Å: Chain F: D.10, Y.11, F.112, G.113 No protein-ligand interaction detected (PLIP) CA.15: 5 residues within 4Å: Chain G: D.32, D.38, D.90, F.91, D.92 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.32, G:D.38, G:F.91 CA.16: 4 residues within 4Å: Chain F: K.184 Chain G: D.32, D.90, D.92 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.32, G:D.90, G:D.92, G:D.92 CA.17: 3 residues within 4Å: Chain G: D.163, D.169, Y.224 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.169, G:Y.224 CA.18: 4 residues within 4Å: Chain G: D.10, Y.11, F.112, G.113 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Q. et al., Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Nature (2015)

Release Date

2015-08-12

Peptides

Vesicle-associated membrane protein 2: A
Syntaxin-1A: B
Synaptosomal-associated protein 25: C
Synaptosomal-associated protein 25: D
Synaptotagmin-1: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
F

Vesicle-associated membrane protein 2

Syntaxin-1A

Synaptosomal-associated protein 25

Synaptosomal-associated protein 25

Synaptotagmin-1

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