SMTL ID : 9b8p.1

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: Q.261, A.281, G.283, C.284, G.285, K.286, T.287, V.288, R.310, E.313, F.475, Q.552, N.553, G.554, Y.555 Chain D: L.398, S.399, R.400 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:A.281, A:G.283, A:C.284, A:G.285, A:K.286, A:T.287, A:T.287, A:V.288, A:R.310, A:E.313, A:Q.552, A:G.554, A:Y.555 Salt bridges: A:K.286, D:R.400, D:R.400 pi-Stacking: A:F.475, A:Y.555

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coupland, C.E. et al., High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles. Science (2024)

Release Date

2024-07-03

Peptides

H(+)-transporting two-sector ATPase: ABC
V-type proton ATPase subunit B, brain isoform: DEF
ATPase H+-transporting V1 subunit D: G
V-type proton ATPase subunit E 1: HIJ
V-type proton ATPase subunit F: K
V-type proton ATPase subunit G: LMN
SidK: OPQ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
Q

P
R

Q
S

H(+)-transporting two-sector ATPase

V-type proton ATPase subunit B, brain isoform

ATPase H+-transporting V1 subunit D

V-type proton ATPase subunit E 1

V-type proton ATPase subunit F

V-type proton ATPase subunit G

SidK

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