SMTL ID : 6xbw.1

Cryo-EM structure of V-ATPase from bovine brain, state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: T.257, R.280, E.283 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.257

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

ADP.2: 17 residues within 4Å: Chain C: A.251, F.252, G.253, C.254, G.255, K.256, T.257, V.258, R.280, F.445, Q.522, N.523, G.524, Y.525 Chain F: L.398, R.400 Ligands: MG.1 15 PLIP interactions: 2 interactions with chain F, 13 interactions with chain C Salt bridges: F:R.400, F:R.400, C:K.256 Hydrogen bonds: C:G.253, C:C.254, C:G.255, C:K.256, C:T.257, C:T.257, C:V.258, C:R.280, C:E.283, C:Q.522, C:G.524 pi-Stacking: C:F.445

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

POV.3: 18 residues within 4Å: Chain R: G.32, F.33, F.35, D.36, V.37, A.38 Chain U: Y.330, V.332, S.333, W.337, T.360 Chain W: Y.10, F.14, F.90 Chain X: Y.10, F.13, F.14 Ligands: POV.17 15 PLIP interactions: 5 interactions with chain X, 2 interactions with chain U, 3 interactions with chain W, 5 interactions with chain R Hydrophobic interactions: X:Y.10, X:Y.10, X:Y.10, X:F.13, X:F.14, W:Y.10, W:F.14, W:F.90, R:F.35, R:V.37 Hydrogen bonds: U:W.337, R:D.36, R:V.37, R:A.38 pi-Cation interactions: U:Y.330 POV.4: 12 residues within 4Å: Chain 3: F.25 Chain R: T.2, G.3, L.4, L.6, L.7 Chain U: L.446 Chain V: I.323, V.324, Y.327 Ligands: OLA.16, POV.18 7 PLIP interactions: 2 interactions with chain R, 1 interactions with chain 3, 4 interactions with chain V Hydrophobic interactions: R:L.6, R:L.7, 3:F.25, V:I.323, V:I.323, V:V.324, V:V.324 POV.5: 12 residues within 4Å: Chain 0: Y.10, F.13, F.14 Chain R: F.29, D.30 Chain U: Y.365, Y.412 Chain Z: Y.10, F.14, L.93 Ligands: POV.6, POV.15 9 PLIP interactions: 1 interactions with chain U, 5 interactions with chain 0, 3 interactions with chain Z pi-Cation interactions: U:Y.412 Hydrophobic interactions: 0:Y.10, 0:Y.10, 0:F.13, 0:F.13, 0:F.14, Z:F.14, Z:L.93 Hydrogen bonds: Z:Y.10 POV.6: 18 residues within 4Å: Chain R: F.15, C.18, V.22, Y.26, F.29, L.31, R.34 Chain U: Y.412, D.415, A.417, G.418, F.419 Chain V: Y.300, Y.304, F.308, I.316 Ligands: POV.5, POV.7 6 PLIP interactions: 3 interactions with chain V, 2 interactions with chain U, 1 interactions with chain R Hydrophobic interactions: V:F.308, R:F.15 pi-Cation interactions: V:Y.300, V:Y.304, U:F.419 Hydrogen bonds: U:Y.412 POV.7: 10 residues within 4Å: Chain R: Y.26, R.34, F.35, D.36, W.39, F.40 Chain U: G.418, F.419, W.425 Ligands: POV.6 13 PLIP interactions: 4 interactions with chain U, 9 interactions with chain R Hydrophobic interactions: U:W.425, U:W.425, R:F.35, R:F.35, R:F.40, R:F.40 Hydrogen bonds: U:F.419, U:F.420, R:R.34 Salt bridges: R:R.34, R:D.36 pi-Cation interactions: R:W.39, R:W.39 POV.14: 20 residues within 4Å: Chain 1: Y.10, F.14, M.17, A.21, F.25, F.90 Chain 2: E.9, Y.10, F.13 Chain V: Y.298, K.299, N.301, Y.304, V.307, F.308, V.311, L.312, M.315, I.316 Ligands: POV.15 15 PLIP interactions: 7 interactions with chain V, 2 interactions with chain 2, 6 interactions with chain 1 Hydrophobic interactions: V:Y.304, V:V.307, V:F.308, V:L.312, V:M.315, V:I.316, 1:F.14, 1:F.14, 1:A.21, 1:F.25, 1:F.90 Hydrogen bonds: V:Y.298, 2:E.9, 1:Y.10 Salt bridges: 2:E.9 POV.15: 16 residues within 4Å: Chain 0: Y.10, F.14, M.17, A.21, F.25, F.90, L.97 Chain 1: Y.10, F.13, F.14 Chain V: Y.298, Y.300, Y.304 Chain Z: L.101 Ligands: POV.5, POV.14 11 PLIP interactions: 4 interactions with chain 0, 2 interactions with chain V, 4 interactions with chain 1, 1 interactions with chain Z Hydrophobic interactions: 0:F.14, 0:A.21, 0:F.25, 0:L.97, 1:F.13, 1:F.13, 1:F.14, Z:L.101 Hydrogen bonds: V:Y.304 pi-Cation interactions: V:Y.298 Salt bridges: 1:E.9 POV.17: 17 residues within 4Å: Chain R: L.19, L.20, G.23, I.24, T.27, F.35 Chain U: S.333, A.334, R.335 Chain X: Y.10, F.14, L.86, F.90 Chain Y: E.9, Y.10, F.13 Ligands: POV.3 8 PLIP interactions: 2 interactions with chain X, 5 interactions with chain R, 1 interactions with chain Y Hydrophobic interactions: X:F.14, R:L.20, R:L.20, R:I.24, R:F.35, R:F.35, Y:F.13 Hydrogen bonds: X:Y.10 POV.18: 18 residues within 4Å: Chain 3: Y.10, F.14 Chain 4: Y.10, F.13, M.17 Chain U: S.421, G.423, I.424, G.427, S.431, L.435 Chain V: F.302, P.305, V.306, L.310, W.313 Ligands: POV.4, OLA.16 9 PLIP interactions: 4 interactions with chain U, 3 interactions with chain V, 2 interactions with chain 3 Hydrophobic interactions: U:I.424, U:L.435, V:V.306, V:V.306, V:W.313, 3:Y.10, 3:F.14 Hydrogen bonds: U:S.421, U:G.423

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

NAG.8: 4 residues within 4Å: Chain U: N.271, S.273, D.282, R.396 3 PLIP interactions: 3 interactions with chain U Hydrogen bonds: U:N.271, U:S.273, U:R.396 NAG.9: 3 residues within 4Å: Chain U: N.294, T.296, M.318 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain U: F.299, N.301 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:N.301 NAG.11: 7 residues within 4Å: Chain U: Y.276, F.315, G.316, T.317, S.347, N.348, W.391 4 PLIP interactions: 4 interactions with chain U Hydrophobic interactions: U:Y.276, U:W.391 Hydrogen bonds: U:F.315, U:T.317 NAG.12: 5 residues within 4Å: Chain R: D.122 Chain U: N.342, N.355, S.357, D.385 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain U: D.302, I.364, F.403, N.404 5 PLIP interactions: 5 interactions with chain U Hydrophobic interactions: U:I.364, U:N.404 Hydrogen bonds: U:D.302, U:F.403, U:N.404

1 x OLA: OLEIC ACID(Non-covalent)

OLA.16: 12 residues within 4Å: Chain 2: L.97, F.108 Chain 3: F.25, L.28 Chain V: I.314, G.317, T.321, V.324, T.325, N.328 Ligands: POV.4, POV.18 6 PLIP interactions: 2 interactions with chain 3, 2 interactions with chain 2, 2 interactions with chain V Hydrophobic interactions: 3:F.25, 3:L.28, 2:L.97, 2:F.108, V:I.314, V:V.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, R. et al., Cryo-EM structures of intact V-ATPase from bovine brain. Nat Commun (2020)

Release Date

2020-08-19

Peptides

V-type proton ATPase catalytic subunit A: ABC
V-type proton ATPase subunit B, brain isoform: DEF
V-type proton ATPase subunit C 1: G
V-type proton ATPase 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
V-type proton ATPase subunit H: P
V-type proton ATPase subunit a: Q
V-type proton ATPase 21 kDa proteolipid subunit: R
V-type proton ATPase subunit d 1: S
V-type proton ATPase subunit e 2: T
V-type proton ATPase subunit S1: U
Renin receptor: V
V-type proton ATPase 16 kDa proteolipid subunit: WXYZ01234
Ribonuclease kappa: 5

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
P

Q
a

R
b

S
d

T
e

U
s

V
r

W
c

X
g

Y
k

Z
l

0
m

1
n

2
o

3
p

4
q

5
f

Membrane

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

V-type proton ATPase subunit B, brain isoform

V-type proton ATPase subunit C 1

V-type proton ATPase subunit D

V-type proton ATPase subunit E 1

V-type proton ATPase subunit F

V-type proton ATPase subunit G

V-type proton ATPase subunit H

V-type proton ATPase subunit a

V-type proton ATPase 21 kDa proteolipid subunit

V-type proton ATPase subunit d 1

V-type proton ATPase subunit e 2

V-type proton ATPase subunit S1

Renin receptor

V-type proton ATPase 16 kDa proteolipid subunit

Ribonuclease kappa

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