SMTL ID : 7unf.1

CryoEM structure of a mEAK7 bound human V-ATPase complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- GLC- GLC: alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC.1: 19 residues within 4Å: Chain A: T.491, W.492, E.499, S.500, Q.504, L.505, D.506, A.508, T.534, S.538, K.597, S.606, Q.607, A.609, P.610, S.611 Chain T: L.63, F.64 Ligands: MAN-MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.606, A:E.499

1 x MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.2: 2 residues within 4Å: Chain A: S.628 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC.1 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.3: 18 residues within 4Å: Chain D: A.251, F.252, G.253, C.254, G.255, K.256, T.257, V.258, R.280, E.283, F.445, Q.522, N.523, G.524 Chain G: L.398, S.399, R.400, K.403 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:A.251, D:G.253, D:G.255, D:K.256, D:T.257, D:T.257, D:T.257, D:V.258, D:Q.522, D:G.524, D:Y.525 Salt bridges: D:K.256, D:R.280, G:R.400, G:R.400 pi-Stacking: D:F.445, D:F.445

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

NAG.4: 2 residues within 4Å: Chain V: N.273, S.275 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:S.275 NAG.5: 3 residues within 4Å: Chain V: N.296, T.298, T.312 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:N.296, V:T.312 NAG.6: 3 residues within 4Å: Chain V: F.301, N.303, F.306 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:N.303 NAG.7: 5 residues within 4Å: Chain V: Y.278, F.317, T.319, S.349, N.350 5 PLIP interactions: 5 interactions with chain V Hydrophobic interactions: V:Y.278, V:F.317 Hydrogen bonds: V:F.317, V:F.317, V:N.350 NAG.8: 2 residues within 4Å: Chain V: N.357, R.387 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:N.357, V:R.387 NAG.9: 3 residues within 4Å: Chain V: S.259, N.261, E.410 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:S.259, V:E.410

9 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.10: 12 residues within 4Å: Chain V: A.419, F.421 Chain W: Y.294, Y.298, F.302, I.310 Chain Z: F.15, A.21, V.22, Y.26, L.31 Ligands: POV.16 7 PLIP interactions: 3 interactions with chain W, 3 interactions with chain Z, 1 interactions with chain V Hydrophobic interactions: W:F.302, W:I.310, Z:F.15, Z:A.21, Z:V.22, V:F.421 pi-Cation interactions: W:Y.294 POV.11: 19 residues within 4Å: Chain 0: Y.10, F.13, M.17 Chain 1: Y.10, F.14, L.97, L.101 Chain V: S.423, G.425, I.426, S.433, L.437, F.440 Chain W: F.296, V.300, N.303, M.304, W.307 Ligands: POV.14 11 PLIP interactions: 3 interactions with chain 1, 6 interactions with chain V, 1 interactions with chain 0, 1 interactions with chain W Hydrophobic interactions: 1:F.14, 1:L.97, 1:L.101, V:I.426, V:L.437, V:F.440, 0:F.13, W:N.303 Hydrogen bonds: V:S.423, V:G.425, V:I.426 POV.12: 15 residues within 4Å: Chain 2: E.9, Y.10, F.13 Chain 3: Y.10, F.14, F.90 Chain W: K.293, N.295, Y.298, V.301, F.302, V.305, L.306, M.309 Ligands: POV.13 5 PLIP interactions: 3 interactions with chain W, 1 interactions with chain 3, 1 interactions with chain 2 Hydrophobic interactions: W:F.302, W:L.306, 3:F.90, 2:Y.10 Hydrogen bonds: W:N.295 POV.13: 11 residues within 4Å: Chain 3: Y.10, F.13, F.14 Chain 4: Y.10, F.14, F.90 Chain W: Y.292, Y.294, Y.298 Ligands: POV.12, POV.16 6 PLIP interactions: 3 interactions with chain 3, 2 interactions with chain 4, 1 interactions with chain W Hydrophobic interactions: 3:Y.10, 3:F.13, 3:F.13, 4:F.14, 4:F.90 pi-Cation interactions: W:Y.292 POV.14: 18 residues within 4Å: Chain 1: F.25, L.28, Y.32, A.35 Chain 2: Y.32, K.36, L.101, F.108, I.112 Chain V: F.440, L.444 Chain W: A.311, L.312, A.315, N.322, M.326 Ligands: POV.11, POV.18 10 PLIP interactions: 3 interactions with chain 2, 2 interactions with chain W, 2 interactions with chain V, 3 interactions with chain 1 Hydrophobic interactions: 2:L.101, 2:F.108, 2:F.108, W:L.312, W:A.315, V:F.440, V:L.444, 1:F.25, 1:F.25, 1:L.28 POV.15: 15 residues within 4Å: Chain V: R.337 Chain X: E.9, Y.10, F.13 Chain Y: Y.10, F.14, F.90 Chain Z: L.20, G.23, V.24, Y.26, T.27, G.32, F.35 Ligands: POV.17 8 PLIP interactions: 6 interactions with chain Z, 1 interactions with chain V, 1 interactions with chain X Hydrophobic interactions: Z:L.20, Z:V.24, Z:Y.26, Z:T.27, Z:T.27, Z:F.35, X:F.13 Hydrogen bonds: V:R.337 POV.16: 10 residues within 4Å: Chain 4: Y.10 Chain 5: Y.10, F.14 Chain V: Y.367, Y.414 Chain Z: C.25, F.29, D.30 Ligands: POV.10, POV.13 6 PLIP interactions: 3 interactions with chain 5, 2 interactions with chain 4, 1 interactions with chain V Hydrophobic interactions: 5:F.14, 4:Y.10, 4:Y.10 Hydrogen bonds: 5:Y.10, 5:Y.10 pi-Cation interactions: V:Y.414 POV.17: 12 residues within 4Å: Chain 6: Y.10 Chain V: Y.332, V.334, S.335, W.339 Chain Y: Y.10, F.13 Chain Z: G.32, F.35, D.36, A.38 Ligands: POV.15 8 PLIP interactions: 5 interactions with chain V, 3 interactions with chain Y Hydrogen bonds: V:V.334, V:S.335, V:S.335 pi-Cation interactions: V:Y.332, V:W.339 Hydrophobic interactions: Y:Y.10, Y:Y.10, Y:F.13 POV.18: 10 residues within 4Å: Chain V: L.448 Chain W: I.317, I.318, Y.321, N.322 Chain Z: G.3, L.4, L.7, G.10 Ligands: POV.14 6 PLIP interactions: 1 interactions with chain V, 3 interactions with chain W, 2 interactions with chain Z Hydrophobic interactions: V:L.448, W:I.317, W:I.318, Z:L.4, Z:L.7 Hydrogen bonds: W:N.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, R. et al., Molecular basis of mEAK7-mediated human V-ATPase regulation. Nat Commun (2022)

Release Date

2022-06-15

Peptides

V-type proton ATPase 116 kDa subunit a 4: A
KIAA1609 protein, isoform CRA_a: B
V-type proton ATPase catalytic subunit A: CDE
V-type proton ATPase subunit B, brain isoform: FGH
V-type proton ATPase subunit D: I
V-type proton ATPase subunit E 1: JKL
V-type proton ATPase subunit G 1: MNO
V-type proton ATPase subunit F: P
V-type proton ATPase subunit C 1: Q
V-type proton ATPase subunit H: R
V-type proton ATPase subunit d 1: S
V-type proton ATPase subunit e 1: T
Ribonuclease kappa: U
V-type proton ATPase subunit S1: V
ATPase H(+)-transporting lysosomal accessory protein 2: W
V-type proton ATPase 16 kDa proteolipid subunit: XY0123456
V-type proton ATPase 21 kDa proteolipid subunit: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
U

C
L

D
M

E
N

F
O

G
P

H
Q

I
D

J
b

K
c

L
d

M
e

N
f

O
g

P
F

Q
C

R
H

S
k

T
m

U
n

V
s

W
r

X
8

Y
9

0
2

1
3

2
4

3
5

4
6

5
7

6
0

Z
1

Membrane

We predict this structure to be a membrane protein.
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V-type proton ATPase 116 kDa subunit a 4

KIAA1609 protein, isoform CRA_a

V-type proton ATPase catalytic subunit A

V-type proton ATPase subunit B, brain isoform

V-type proton ATPase subunit D

V-type proton ATPase subunit E 1

V-type proton ATPase subunit G 1

V-type proton ATPase subunit F

V-type proton ATPase subunit C 1

V-type proton ATPase subunit H

V-type proton ATPase subunit d 1

V-type proton ATPase subunit e 1

Ribonuclease kappa

V-type proton ATPase subunit S1

ATPase H(+)-transporting lysosomal accessory protein 2

V-type proton ATPase 16 kDa proteolipid subunit

V-type proton ATPase 21 kDa proteolipid subunit

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