SMTL ID : 9cop.1

Yeast RAVE bound to V-ATPase V1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-1-1-1-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.263, T.264, E.740, D.810 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.264 MG.3: 6 residues within 4Å: Chain C: K.263, T.264, E.740, D.810, S.811 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.810

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

ADP.2: 21 residues within 4Å: Chain A: Q.238, A.258, F.259, G.260, C.261, G.262, K.263, T.264, V.265, I.266, F.906, P.907, Q.983, N.984, G.985, Y.986 Chain B: L.379, S.380, R.381, K.384 Ligands: MG.1 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.258, A:G.260, A:C.261, A:G.262, A:K.263, A:T.264, A:V.265, A:G.985 Salt bridges: A:K.263, B:R.381, B:R.381 pi-Stacking: A:F.906 ADP.4: 23 residues within 4Å: Chain C: Q.238, A.258, F.259, G.260, C.261, G.262, K.263, T.264, V.265, I.266, R.741, E.744, K.904, F.906, P.907, Q.983, N.984, G.985, Y.986 Chain D: L.379, R.381, K.384 Ligands: MG.3 17 PLIP interactions: 3 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:R.381, D:R.381, C:A.258, C:C.261, C:G.262, C:K.263, C:T.264, C:V.265, C:R.741, C:E.744, C:Q.983, C:G.985 Salt bridges: D:R.381, C:K.263 pi-Stacking: C:F.906, C:F.906, C:Y.986

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structure of yeast RAVE bound to a partial V1 complex. To Be Published

Release Date

2024-11-20

Peptides

V-type proton ATPase catalytic subunit A: AC
V-type proton ATPase subunit B: BD
V-type proton ATPase subunit E: EG
V-type proton ATPase subunit G: FH
V-type proton ATPase subunit D: I
V-type proton ATPase subunit F: J
V-type proton ATPase subunit H: K
Regulator of V-ATPase in vacuolar membrane protein 1: L
Regulator of V-ATPase in vacuolar membrane protein 2: M
Suppressor of kinetochore protein 1: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
E

B
B

D
F

E
I

G
K

F
J

H
L

I
M

J
N

K
P

L
x

M
y

N
z

V-type proton ATPase catalytic subunit A

V-type proton ATPase subunit B

V-type proton ATPase subunit E

V-type proton ATPase subunit G

V-type proton ATPase subunit D

V-type proton ATPase subunit F

V-type proton ATPase subunit H

Regulator of V-ATPase in vacuolar membrane protein 1

Regulator of V-ATPase in vacuolar membrane protein 2

Suppressor of kinetochore protein 1

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