SMTL ID : 6xby.1

Cryo-EM structure of V-ATPase from bovine brain, state 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.257, R.280 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.257

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

ADP.2: 16 residues within 4Å: Chain A: A.251, F.252, G.253, C.254, G.255, K.256, T.257, V.258, R.280, E.283, F.445, Q.522, G.524, Y.525 Chain D: R.400 Ligands: MG.1 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.253, A:C.254, A:G.255, A:K.256, A:T.257, A:T.257, A:V.258, A:R.280, A:Q.522, A:G.524, A:Y.525, A:Y.525 Salt bridges: A:K.256, A:R.280, D:R.400, D:R.400 pi-Stacking: A:F.445, A:Y.525

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

POV.3: 15 residues within 4Å: Chain 2: Y.330, V.332, S.333, W.337, T.360 Chain R: G.32, F.33, F.35, D.36, V.37, A.38 Chain V: Y.10, F.90 Chain W: Y.10, F.13 13 PLIP interactions: 5 interactions with chain 2, 4 interactions with chain R, 2 interactions with chain V, 2 interactions with chain W Hydrophobic interactions: 2:V.332, R:F.35, R:V.37, R:V.37, R:A.38, V:Y.10, V:F.90, W:Y.10, W:F.13 Hydrogen bonds: 2:S.333, 2:W.337 pi-Cation interactions: 2:Y.330, 2:W.337 POV.4: 9 residues within 4Å: Chain 2: Y.412 Chain R: F.29, D.30 Chain Y: Y.10, F.14 Chain Z: Y.10, F.13 Ligands: POV.6, POV.15 5 PLIP interactions: 2 interactions with chain Z, 2 interactions with chain Y, 1 interactions with chain 2 Hydrophobic interactions: Z:Y.10, Z:F.13, Y:F.14 Hydrogen bonds: Y:Y.10 pi-Cation interactions: 2:Y.412 POV.5: 17 residues within 4Å: Chain 0: Y.10, F.14, L.86, F.90 Chain 1: E.9, Y.10, F.13 Chain 3: Y.298, K.299, N.301, Y.304, V.307, F.308, V.311, L.312, M.315 Ligands: POV.15 10 PLIP interactions: 7 interactions with chain 3, 2 interactions with chain 0, 1 interactions with chain 1 Hydrophobic interactions: 3:Y.304, 3:V.307, 3:F.308, 3:F.308, 3:V.311, 3:L.312, 0:F.14, 0:F.90, 1:F.13 Hydrogen bonds: 3:N.301 POV.6: 20 residues within 4Å: Chain 2: Y.412, D.415, A.417, G.418, F.419, F.420 Chain 3: Y.300, Y.304, I.316 Chain R: V.11, F.15, A.17, C.18, V.21, V.22, Y.26, F.29, L.31, R.34 Ligands: POV.4 13 PLIP interactions: 3 interactions with chain 3, 7 interactions with chain R, 3 interactions with chain 2 Hydrophobic interactions: 3:I.316, R:V.11, R:F.15, R:A.17, R:V.21, R:V.22, R:V.22, 2:F.419, 2:F.420 pi-Cation interactions: 3:Y.300, 3:Y.304 Salt bridges: R:R.34 Hydrogen bonds: 2:Y.412 POV.13: 18 residues within 4Å: Chain 2: D.378, S.421, G.423, I.424, G.427, S.431, M.434 Chain 3: F.302, V.306, N.309, W.313, I.314 Chain T: Y.10, F.13, M.17 Chain U: Y.10, F.14, F.90 11 PLIP interactions: 3 interactions with chain U, 4 interactions with chain 2, 3 interactions with chain 3, 1 interactions with chain T Hydrophobic interactions: U:F.14, U:F.14, U:F.90, 2:I.424, 3:N.309, 3:I.314, T:F.13 Hydrogen bonds: 2:D.378, 2:S.421, 2:G.423, 3:N.309 POV.14: 10 residues within 4Å: Chain 2: L.446 Chain 3: L.320, I.323, V.324, Y.327 Chain R: G.3, L.4, L.6, L.7, G.10 8 PLIP interactions: 6 interactions with chain 3, 2 interactions with chain R Hydrophobic interactions: 3:L.320, 3:L.320, 3:I.323, 3:V.324, 3:Y.327, 3:Y.327, R:L.6, R:L.7 POV.15: 15 residues within 4Å: Chain 0: E.9, Y.10, F.13, F.14 Chain 3: Y.298, Y.300, Y.304 Chain Z: Y.10, F.14, M.17, A.21, F.25, F.90 Ligands: POV.4, POV.5 9 PLIP interactions: 2 interactions with chain 3, 5 interactions with chain Z, 2 interactions with chain 0 Hydrogen bonds: 3:Y.304 pi-Cation interactions: 3:Y.298 Hydrophobic interactions: Z:F.14, Z:F.14, Z:A.21, Z:F.25, Z:F.90, 0:F.13, 0:F.14

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

NAG.7: 2 residues within 4Å: Chain 2: N.271, D.282 No protein-ligand interaction detected (PLIP) NAG.8: 5 residues within 4Å: Chain 2: N.294, T.296, T.310, D.312, M.318 1 PLIP interactions: 1 interactions with chain 2 Hydrogen bonds: 2:T.310 NAG.9: 2 residues within 4Å: Chain 2: F.299, N.301 1 PLIP interactions: 1 interactions with chain 2 Hydrogen bonds: 2:N.301 NAG.10: 5 residues within 4Å: Chain 2: Y.276, F.315, T.317, N.348, W.391 4 PLIP interactions: 4 interactions with chain 2 Hydrophobic interactions: 2:Y.276, 2:W.391 Hydrogen bonds: 2:F.315, 2:T.317 NAG.11: 4 residues within 4Å: Chain 2: N.342, N.355, D.385 Chain R: D.122 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain 2: D.302, I.364, F.403, N.404 4 PLIP interactions: 4 interactions with chain 2 Hydrophobic interactions: 2:I.364, 2:N.404 Hydrogen bonds: 2:D.302, 2:F.403

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 16 kDa proteolipid subunit: TUVWXYZ01
V-type proton ATPase subunit S1: 2
Renin receptor: 3

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
q

U
p

V
c

W
g

X
k

Y
l

Z
m

0
n

1
o

2
s

3
r

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 16 kDa proteolipid subunit

V-type proton ATPase subunit S1

Renin receptor

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