SMTL ID : 6mti.1

Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-4-6-6-6-6-mer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.32, D.38, F.91, D.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.32, A:D.38, A:F.91, A:D.92 MG.2: 4 residues within 4Å: Chain B: D.32, D.38, F.91, D.92 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.32, B:D.38, B:F.91, B:D.92 MG.3: 5 residues within 4Å: Chain B: D.163, D.169, D.223, Y.224, D.225 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.163, B:D.163, B:D.169, B:D.223, B:D.225 MG.4: 4 residues within 4Å: Chain C: D.32, D.38, F.91, D.92 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.32, C:D.38, C:F.91, C:D.92 MG.5: 5 residues within 4Å: Chain C: D.163, D.169, D.223, Y.224, D.225 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.163, C:D.163, C:D.169, C:D.223, C:D.225 MG.6: 4 residues within 4Å: Chain D: D.32, D.38, F.91, D.92 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.32, D:D.38, D:F.91, D:D.92 MG.7: 5 residues within 4Å: Chain D: D.163, D.169, D.223, Y.224, D.225 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.163, D:D.163, D:D.169, D:D.223, D:D.225 MG.8: 4 residues within 4Å: Chain E: D.32, D.38, F.91, D.92 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.32, E:D.38, E:F.91, E:D.92 MG.9: 5 residues within 4Å: Chain E: D.163, D.169, D.223, Y.224, D.225 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.163, E:D.163, E:D.169, E:D.223, E:D.225 MG.10: 4 residues within 4Å: Chain F: D.32, D.38, F.91, D.92 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.32, F:D.38, F:F.91, F:D.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grushin, K. et al., Structural basis for the clamping and Ca2+activation of SNARE-mediated fusion by synaptotagmin. Nat Commun (2019)

Release Date

2019-04-24

Peptides

Synaptotagmin-1: AF
Synaptotagmin-1: BCDE
Vesicle-associated membrane protein 2: GKOSW0
Syntaxin-1A: HLPTX1
Synaptosomal-associated protein 25: IMQUY2
Synaptosomal-associated protein 25: JNRVZ3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

F
6

B
2

C
3

D
4

E
5

G
A

K
E

O
I

S
M

W
Q

0
U

H
B

L
F

P
J

T
N

X
R

1
V

I
C

M
G

Q
K

U
O

Y
S

2
W

J
D

N
H

R
L

V
P

Z
T

3
X

Synaptotagmin-1

Synaptotagmin-1

Vesicle-associated membrane protein 2

Syntaxin-1A

Synaptosomal-associated protein 25

Synaptosomal-associated protein 25

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