SMTL ID : 9bry.1

V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-9-1-1-1-mer

Ligands

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 3 residues within 4Å: Chain A: H.349, N.351, T.380 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: F.311, N.344 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: N.267, F.268, S.269, W.276, D.278, L.279, T.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.269, A:S.269

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 2 residues within 4Å: Chain A: N.290, T.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.290, A:T.292 NAG.6: 3 residues within 4Å: Chain A: F.295, N.297, F.300 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: S.253, N.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.255 NAG.8: 4 residues within 4Å: Chain A: D.298, Y.332, F.398, N.399 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.332 Hydrogen bonds: A:F.398

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.5: 3 residues within 4Å: Chain A: A.313, T.314, S.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.314, A:T.314, A:H.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Structure and topography of the synaptic V-ATPase-synaptophysin complex. Nature (2024)

Release Date

2024-06-19

Peptides

V-type proton ATPase subunit S1: A
V-type proton ATPase 21 kDa proteolipid subunit c'': B
V-type proton ATPase subunit d 1: C
Ribonuclease kappa: D
V-type proton ATPase 16 kDa proteolipid subunit c: EFGHIJKLM
Renin receptor cytoplasmic fragment: N
V-type proton ATPase subunit e 2: O
V-type proton ATPase 116 kDa subunit a 1: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
c

B
b

C
d

D
f

E
g

F
h

G
i

H
j

I
k

J
l

K
m

L
n

M
o

N
p

O
e

P
a

Membrane

We predict this structure to be a membrane protein.
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V-type proton ATPase subunit S1

V-type proton ATPase 21 kDa proteolipid subunit c''

V-type proton ATPase subunit d 1

Ribonuclease kappa

V-type proton ATPase 16 kDa proteolipid subunit c

Renin receptor cytoplasmic fragment

V-type proton ATPase subunit e 2

V-type proton ATPase 116 kDa subunit a 1

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