SMTL ID : 6vq7.1

Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-3-1-3-3-1-1-1-1-1-1-9-1-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain B: A.251, F.252, G.253, C.254, G.255, K.256, T.257, V.258, F.445, Q.522, N.523, G.524, Y.525 Chain E: L.398, R.400, K.403 Ligands: MG.2 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:A.251, B:G.253, B:C.254, B:G.255, B:K.256, B:T.257, B:T.257, B:V.258, B:R.280, B:G.524, E:K.403 pi-Stacking: B:F.445 Salt bridges: E:R.400, E:R.400

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: T.257, E.279 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abbas, Y.M. et al., Structure of V-ATPase from the mammalian brain. Science (2020)

Release Date

2020-03-18

Peptides

ATPase H+-transporting V1 subunit A: ABC
V-type proton ATPase subunit B, brain isoform: DEF
V-type proton ATPase subunit C 1: G
ATPase H+-transporting V1 subunit D: H
V-type proton ATPase subunit E 1: IJK
V-type proton ATPase subunit F: L
V-type proton ATPase subunit G: MNO
Effector protein SidK: PQR
V-type proton ATPase 116 kDa subunit a isoform 1: S
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a: T
V-type proton ATPase subunit S1: U
V-type proton ATPase subunit: V
V-type proton ATPase subunit e 2: W
Ribonuclease K: X
V-type proton ATPase 16 kDa proteolipid subunit: YZ0123456
Renin receptor: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
Q

Q
R

R
S

S
a

T
b

U
c

V
d

W
e

X
f

Y
g

Z
h

0
i

1
j

2
k

3
l

4
m

5
n

6
o

7
p

Membrane

We predict this structure to be a membrane protein.
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ATPase H+-transporting V1 subunit A

V-type proton ATPase subunit B, brain isoform

V-type proton ATPase subunit C 1

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

Effector protein SidK

V-type proton ATPase 116 kDa subunit a isoform 1

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

V-type proton ATPase subunit S1

V-type proton ATPase subunit

V-type proton ATPase subunit e 2

Ribonuclease K

V-type proton ATPase 16 kDa proteolipid subunit

Renin receptor

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