SMTL ID : 7tao.1

Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-8-1-1-1-mer

Ligands

9 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)

WEV.1: 12 residues within 4Å: Chain A: M.57, K.58, I.61, V.64, I.71 Chain B: V.186, I.189, F.190, I.193 Chain O: I.713, V.716, I.720 12 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, 3 interactions with chain O Hydrophobic interactions: B:V.186, B:F.190, B:F.190, B:I.193, A:I.61, A:V.64, A:V.64, A:V.64, A:I.71, O:I.713, O:I.720, O:I.720 WEV.2: 10 residues within 4Å: Chain A: L.139, I.142, F.143, V.146, Y.150 Chain E: F.51, I.54, I.58, G.61, I.65 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:L.139, A:I.142, A:F.143, E:I.54, E:I.58, E:I.58, E:I.65 WEV.3: 9 residues within 4Å: Chain E: L.131, I.134, F.135, Y.142 Chain G: F.51, I.54, V.55, I.58, I.65 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:F.51, G:I.54, G:V.55, G:I.65, E:F.135 WEV.4: 9 residues within 4Å: Chain G: L.131, F.135, V.138, Y.142 Chain H: F.51, I.54, I.58, G.61, I.65 7 PLIP interactions: 4 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:F.135, G:F.135, G:V.138, H:I.54, H:I.58, H:I.65 Hydrogen bonds: G:Y.142 WEV.5: 7 residues within 4Å: Chain H: I.134, F.135, V.138, Y.142 Chain I: F.51, I.58, I.65 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain H Hydrophobic interactions: I:F.51, I:I.58, I:I.58, H:I.134, H:F.135, H:V.138 WEV.6: 9 residues within 4Å: Chain I: L.131, I.134, F.135, V.138, Y.142 Chain J: F.51, I.54, I.58, I.65 9 PLIP interactions: 3 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: J:I.54, J:I.58, J:I.65, I:I.134, I:F.135, I:F.135, I:V.138 Hydrogen bonds: I:Y.142, I:Y.142 WEV.7: 11 residues within 4Å: Chain J: L.131, I.134, F.135, V.138, Y.142 Chain K: F.51, I.54, V.55, I.58, G.61, I.65 9 PLIP interactions: 6 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: K:F.51, K:F.51, K:I.54, K:V.55, K:I.58, K:I.65, J:F.135, J:F.135, J:V.138 WEV.8: 11 residues within 4Å: Chain K: L.131, I.134, F.135, Y.142 Chain L: F.51, K.52, I.54, V.55, I.58, G.61, I.65 13 PLIP interactions: 4 interactions with chain K, 9 interactions with chain L Hydrophobic interactions: K:L.131, K:F.135, K:F.135, L:F.51, L:F.51, L:I.54, L:V.55, L:I.58, L:I.58, L:I.65 Hydrogen bonds: K:Y.142, L:K.52, L:G.61 WEV.9: 16 residues within 4Å: Chain L: L.131, I.134, F.135, V.138, Y.142 Chain M: F.51, I.54, V.55, I.58, G.61, I.65 Chain O: I.454, L.780, A.783, V.784, L.787 13 PLIP interactions: 4 interactions with chain O, 3 interactions with chain L, 6 interactions with chain M Hydrophobic interactions: O:I.454, O:L.780, O:A.783, O:V.784, L:I.134, L:F.135, L:F.135, M:F.51, M:F.51, M:I.54, M:V.55, M:I.58, M:I.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keon, K.A. et al., Cryo-EM of the Yeast V O Complex Reveals Distinct Binding Sites for Macrolide V-ATPase Inhibitors. Acs Chem.Biol. (2022)

Release Date

2022-02-23

Peptides

V-type proton ATPase subunit c': A
V-type proton ATPase subunit c'': B
V0 assembly protein 1: C
V-type proton ATPase subunit e: D
V-type proton ATPase subunit c: EGHIJKLM
Yeast V-ATPase subunit f: F
V-type proton ATPase subunit d: N
V-type proton ATPase subunit a, vacuolar isoform: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
N

D
M

E
E

G
F

H
G

I
H

J
I

K
J

L
K

M
L

F
O

N
B

O
A

Membrane

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

V-type proton ATPase subunit c''

V0 assembly protein 1

V-type proton ATPase subunit e

V-type proton ATPase subunit c

Yeast V-ATPase subunit f

V-type proton ATPase subunit d

V-type proton ATPase subunit a, vacuolar isoform

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