SMTL ID : 7khr.1

Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain

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 NAG- NAG- BMA- MAN- MAN- MAN- GLC- GLC- GLC: alpha-D-glucopyranose-(1-2)-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-GLC.1: 20 residues within 4Å: Chain Q: Y.488, W.490, E.493, R.496, G.497, N.498, Q.502, L.503, N.504, T.531, S.535, K.594, A.600, E.604, A.606, P.607 Chain T: L.63, F.64 Ligands: MAN-MAN.2, WJP.5 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:E.493

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

MAN-MAN.2: 4 residues within 4Å: Chain Q: K.605, G.625 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC.1, NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC.1 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.626

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain C: T.257, R.280, E.283 Ligands: ADP.4 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.257, C:E.283, C:E.283

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

ADP.4: 17 residues within 4Å: Chain C: 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, Y.525 Chain F: R.400, K.403 Ligands: MG.3 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:G.253, C:C.254, C:G.255, C:K.256, C:T.257, C:T.257, C:V.258, C:Q.522, C:G.524 Salt bridges: C:K.256, C:R.280, C:R.280, F:R.400, F:R.400 pi-Stacking: C:F.445, C:Y.525

1 x WJP: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate(Non-covalent)

WJP.5: 16 residues within 4Å: Chain 1: L.150 Chain Q: S.535, K.539, V.542, F.584, I.591, K.594, S.608, L.609, L.610, F.613, I.614, I.733, T.736, A.737 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC.1 17 PLIP interactions: 16 interactions with chain Q, 1 interactions with chain 1 Hydrophobic interactions: Q:K.539, Q:V.542, Q:F.584, Q:I.591, Q:L.610, Q:F.613, Q:I.614, Q:I.733, Q:T.736, Q:A.737, 1:L.150 Hydrogen bonds: Q:L.609, Q:L.610 Salt bridges: Q:K.539, Q:K.539, Q:K.594, Q:K.594

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

POV.6: 16 residues within 4Å: Chain R: F.15, V.21, V.22, C.25, Y.26, F.29, L.31, R.34 Chain U: Y.412, D.415, G.418, F.419 Chain V: Y.300, Y.304, I.316 Ligands: POV.23 8 PLIP interactions: 5 interactions with chain U, 2 interactions with chain V, 1 interactions with chain R Hydrophobic interactions: U:F.419, U:F.419, V:I.316, R:F.15 Hydrogen bonds: U:Y.412 Salt bridges: U:D.415 pi-Cation interactions: U:F.419, V:Y.300 POV.7: 20 residues within 4Å: Chain R: W.16, L.20, G.23, I.24, Y.26, T.27, D.30, G.32, 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.8 11 PLIP interactions: 3 interactions with chain Y, 4 interactions with chain R, 4 interactions with chain X Hydrophobic interactions: Y:Y.10, Y:F.13, R:W.16, R:L.20, R:F.35, X:F.14, X:F.90 Salt bridges: Y:E.9 Hydrogen bonds: R:D.30, X:Y.10, X:Y.10 POV.8: 15 residues within 4Å: Chain R: G.32, F.33, D.36, 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 Ligands: POV.7 12 PLIP interactions: 2 interactions with chain R, 2 interactions with chain W, 4 interactions with chain U, 4 interactions with chain X Hydrogen bonds: R:D.36, R:V.37, U:V.332, U:S.333 Hydrophobic interactions: W:Y.10, W:F.14, U:V.332, X:Y.10, X:Y.10, X:Y.10, X:F.13 pi-Cation interactions: U:Y.330 POV.9: 19 residues within 4Å: Chain 3: Y.10, F.13, F.14, F.90 Chain 4: Y.10, F.13 Chain U: D.378, S.421, G.423, I.424, G.427, S.431 Chain V: F.302, P.305, V.306, N.309, L.310, W.313 Ligands: OLA.20 11 PLIP interactions: 5 interactions with chain U, 2 interactions with chain V, 1 interactions with chain 4, 3 interactions with chain 3 Hydrophobic interactions: U:I.424, V:V.306, V:N.309, 4:F.13, 3:F.13, 3:F.13, 3:F.14 Hydrogen bonds: U:D.378, U:S.421, U:G.423 Salt bridges: U:D.378 POV.17: 17 residues within 4Å: Chain 1: Y.10, F.14, M.17, S.20, A.21, F.90 Chain 2: Y.10, F.13 Chain V: Y.298, K.299, N.301, Y.304, V.307, F.308, V.311, I.316 Ligands: POV.19 13 PLIP interactions: 5 interactions with chain 1, 6 interactions with chain V, 2 interactions with chain 2 Hydrophobic interactions: 1:F.14, 1:F.14, 1:F.90, V:Y.304, V:V.307, V:F.308, V:V.311, V:I.316, 2:F.13, 2:F.13 Hydrogen bonds: 1:Y.10, 1:Y.10, V:N.301 POV.18: 14 residues within 4Å: Chain 3: F.25 Chain R: G.3, L.4, L.6, L.7, G.10 Chain U: L.446 Chain V: L.320, T.321, I.323, V.324, Y.327, N.328 Ligands: OLA.20 6 PLIP interactions: 5 interactions with chain V, 1 interactions with chain 3 Hydrophobic interactions: V:L.320, V:I.323, V:V.324, V:V.324, V:Y.327, 3:F.25 POV.19: 13 residues within 4Å: Chain 0: Y.10, F.14, M.17, S.20, A.21, L.97 Chain 1: Y.10, F.13, F.14 Chain V: Y.298, Y.300, Y.304 Ligands: POV.17 6 PLIP interactions: 2 interactions with chain V, 3 interactions with chain 0, 1 interactions with chain 1 Hydrogen bonds: V:Y.304 pi-Cation interactions: V:Y.298 Hydrophobic interactions: 0:F.14, 0:A.21, 0:L.97, 1:F.13 POV.23: 8 residues within 4Å: Chain 0: Y.10 Chain R: F.29, D.30 Chain U: Y.365, Y.412 Chain Z: Y.10, F.14 Ligands: POV.6 4 PLIP interactions: 1 interactions with chain U, 2 interactions with chain Z, 1 interactions with chain 0 pi-Cation interactions: U:Y.412 Hydrophobic interactions: Z:F.14, 0:Y.10 Hydrogen bonds: Z:Y.10

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

NAG.10: 2 residues within 4Å: Chain U: N.271, S.273 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:S.273 NAG.11: 3 residues within 4Å: Chain U: N.294, T.296, D.312 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:N.294, U:N.294 NAG.12: 2 residues within 4Å: Chain U: F.299, N.301 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:N.301 NAG.13: 5 residues within 4Å: Chain U: Y.276, F.315, T.317, S.347, N.348 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:F.315 NAG.14: 4 residues within 4Å: Chain R: D.122 Chain U: N.342, N.355, D.385 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:N.342 NAG.15: 4 residues within 4Å: Chain U: D.302, I.364, F.403, N.404 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:F.403, U:N.404 NAG.16: 2 residues within 4Å: Chain U: N.258, S.260 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:N.258

1 x OLA: OLEIC ACID(Non-covalent)

OLA.20: 12 residues within 4Å: Chain 2: L.97, F.108 Chain 3: F.25, L.28 Chain V: I.314, G.317, L.318, T.321, V.324, N.328 Ligands: POV.9, POV.18 7 PLIP interactions: 4 interactions with chain V, 2 interactions with chain 3, 1 interactions with chain 2 Hydrophobic interactions: V:I.314, V:L.318, V:T.321, V:V.324, 3:F.25, 3:L.28, 2:L.97

6 x WEV: (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose(Non-covalent)(Covalent)

WEV.21: 8 residues within 4Å: Chain W: L.133, F.137, Y.144 Chain X: M.53, I.56, I.57, V.60, I.64 7 PLIP interactions: 3 interactions with chain X, 4 interactions with chain W Hydrophobic interactions: X:I.56, X:I.57, X:I.64, W:L.133, W:F.137, W:F.137 Hydrogen bonds: W:Y.144 WEV.22: 6 residues within 4Å: Chain X: I.136, F.137, Y.144 Chain Y: M.53, V.60, I.64 5 PLIP interactions: 3 interactions with chain Y, 2 interactions with chain X Hydrophobic interactions: Y:V.60, Y:I.64, X:I.136, X:F.137 Hydrogen bonds: Y:G.63 WEV.24: 8 residues within 4Å: Chain Y: L.133, F.137, Y.144 Chain Z: M.53, I.57, V.60, I.64, I.67 4 PLIP interactions: 2 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:L.133, Y:F.137, Z:V.60, Z:I.64 WEV.25: 7 residues within 4Å: Chain 0: M.53, I.57 Chain Z: L.133, I.136, F.137, V.140, Y.144 8 PLIP interactions: 2 interactions with chain 0, 6 interactions with chain Z Hydrophobic interactions: 0:I.57, 0:I.57, Z:L.133, Z:I.136, Z:F.137, Z:F.137, Z:V.140 Hydrogen bonds: Z:Y.144 WEV.26: 5 residues within 4Å: Chain 2: L.133, I.136, F.137 Chain 3: M.53, I.64 5 PLIP interactions: 4 interactions with chain 2, 1 interactions with chain 3 Hydrophobic interactions: 2:L.133, 2:I.136, 2:F.137, 2:F.137, 3:M.53 WEV.27: 8 residues within 4Å: Chain 3: L.133, I.136, F.137, V.140, Y.144 Chain 4: M.53, V.60, I.64 4 PLIP interactions: 2 interactions with chain 3, 2 interactions with chain 4 Hydrophobic interactions: 3:I.136, 3:F.137, 4:V.60, 4:I.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, R. et al., Molecular basis of V-ATPase inhibition by bafilomycin A1. Nat Commun (2021)

Release Date

2021-03-17

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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