SMTL ID : 7u4t.1

Human V-ATPase in state 2 with SidK and mEAK-7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 2 residues within 4Å: Chain A: Y.487, N.488 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.487 NAG.2: 4 residues within 4Å: Chain A: L.494, R.495 Chain I: N.70 Chain J: F.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.495, A:R.495 NAG.3: 4 residues within 4Å: Chain K: Y.278, F.317, T.319, N.350 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:F.317, K:T.319 Hydrogen bonds: K:T.319, K:T.319 NAG.4: 2 residues within 4Å: Chain K: N.296, T.298 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.296 NAG.5: 3 residues within 4Å: Chain K: S.259, N.261, Q.293 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:S.259, K:N.261, K:Q.293 NAG.6: 1 residues within 4Å: Chain K: N.303 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.303 NAG.7: 2 residues within 4Å: Chain K: N.357, R.387 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.357, K:R.387 NAG.8: 4 residues within 4Å: Chain K: N.273, S.275, D.284, M.396 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.275

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

ADP.9: 16 residues within 4Å: Chain 1: R.400, K.403 Chain Z: A.251, F.252, G.253, G.255, K.256, T.257, V.258, R.280, E.283, F.445, Q.522, N.523, G.524, Y.525 15 PLIP interactions: 13 interactions with chain Z, 2 interactions with chain 1 Hydrogen bonds: Z:G.253, Z:C.254, Z:G.255, Z:K.256, Z:T.257, Z:T.257, Z:V.258, Z:R.280, Z:E.283, Z:Q.522, Z:G.524 Salt bridges: Z:K.256, 1:R.400, 1:R.400 pi-Stacking: Z:F.445

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Identification of mEAK-7 as a human V-ATPase regulator via cryo-EM data mining. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-08-24

Peptides

V-type proton ATPase 116 kDa subunit a isoform 1: A
V-type proton ATPase subunit C 1: B
V-type proton ATPase subunit E 1: CEG
V-type proton ATPase subunit G 1: DFH
V-type proton ATPase subunit e 1: I
Ribonuclease kappa: J
V-type proton ATPase subunit S1: K
Renin receptor: L
V-type proton ATPase 21 kDa proteolipid subunit: M
V-type proton ATPase 16 kDa proteolipid subunit: NOPQRSTUV
V-type proton ATPase subunit d 1: W
V-type proton ATPase catalytic subunit A: XYZ
V-type proton ATPase subunit B, brain isoform: 019
SidK: 234
V-type proton ATPase subunit D: 5
V-type proton ATPase subunit F: 6
V-type proton ATPase subunit H: 7
MTOR-associated protein MEAK7: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
O

C
J

E
I

G
H

D
M

F
L

H
K

I
S

J
T

K
U

L
V

M
0

N
1

O
2

P
3

Q
4

R
5

S
6

T
7

U
8

V
9

W
Q

X
C

Y
A

Z
B

0
D

1
E

9
F

2
Z

3
X

4
Y

5
G

6
N

7
P

8
W

Membrane

We predict this structure to be a membrane protein.
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V-type proton ATPase 116 kDa subunit a isoform 1

V-type proton ATPase subunit C 1

V-type proton ATPase subunit E 1

V-type proton ATPase subunit G 1

V-type proton ATPase subunit e 1

Ribonuclease kappa

V-type proton ATPase subunit S1

Renin receptor

V-type proton ATPase 21 kDa proteolipid subunit

V-type proton ATPase 16 kDa proteolipid subunit

V-type proton ATPase subunit d 1

V-type proton ATPase catalytic subunit A

V-type proton ATPase subunit B, brain isoform

SidK

V-type proton ATPase subunit D

V-type proton ATPase subunit F

V-type proton ATPase subunit H

MTOR-associated protein MEAK7

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