SMTL ID : 8qqk.1

Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

POV.1: 15 residues within 4Å: Chain A: F.138, P.139, F.140, L.141, L.144, I.199, F.602, F.618, W.625 Chain C: K.25, G.28, F.29, Y.32 Ligands: 3PE.4, POV.8 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:F.29, C:Y.32, A:F.138, A:L.141, A:L.144, A:F.602, A:F.618, A:W.625, A:W.625 Salt bridges: C:K.25 Hydrogen bonds: A:F.140, A:L.141 POV.2: 14 residues within 4Å: Chain A: Y.37, W.41, Y.43, W.48, I.59, M.60, I.62, I.63, M.436, W.440, F.444, M.516, I.520, R.523 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.48, A:W.48, A:I.62, A:I.63, A:W.440, A:F.444, A:F.444 Hydrogen bonds: A:Y.37 Salt bridges: A:R.523 POV.8: 17 residues within 4Å: Chain A: F.618, I.622, W.625, I.626, K.628, S.629 Chain C: K.25, F.29, Y.32, T.145, H.149, S.152, W.156, R.176, F.183 Ligands: POV.1, 3PE.4 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.618, A:I.622, A:W.625, A:W.625, A:I.626, C:W.156, C:W.156, C:F.183 Salt bridges: C:K.25, C:R.176, C:R.176

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-functional Binders)(Non-covalent)

3PE.3: 2 residues within 4Å: Ligands: 3PE.4, 3PE.9 No protein-ligand interaction detected (PLIP) 3PE.4: 11 residues within 4Å: Chain A: T.254, L.255, Y.258, L.259, M.606, W.611, I.615, F.618 Ligands: POV.1, 3PE.3, POV.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.254, A:L.255, A:Y.258, A:L.259, A:W.611, A:I.615, A:F.618 3PE.9: 10 residues within 4Å: Chain A: L.259 Chain C: F.120, H.121, I.124, P.130, F.140, G.144, T.145, G.147 Ligands: 3PE.3 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.120, C:P.130

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.5: 23 residues within 4Å: Chain A: F.73, A.76, M.79, R.80, Q.83, F.103, H.106, G.107, M.110, I.111, G.169, W.170, L.414, I.417, F.420, H.421, I.424, I.425, V.429, F.468, R.481, R.482, I.505 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:F.73, A:A.76, A:M.110, A:I.111, A:I.111, A:W.170, A:I.417, A:F.420, A:F.420, A:I.424, A:I.425, A:V.429, A:I.505 Hydrogen bonds: A:Q.83, A:Q.83, A:W.170, A:R.482 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:H.106, A:F.420, A:H.421, A:F.468 Metal complexes: A:H.106, A:H.421

1 x HEO: HEME O(Non-covalent)

HEO.6: 35 residues within 4Å: Chain A: W.170, W.280, H.284, V.287, Y.288, L.290, I.291, H.333, H.334, T.352, I.355, A.356, T.359, G.360, I.363, F.391, S.392, G.395, G.398, V.399, L.401, A.402, D.407, H.411, L.416, H.419, F.420, V.423, I.424, V.428, R.481 Chain B: M.51, V.54, I.100 Ligands: CU.7 32 PLIP interactions: 28 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:L.290, A:I.291, A:H.333, A:T.359, A:I.363, A:F.391, A:F.391, A:V.399, A:L.401, A:L.401, A:L.416, A:F.420, A:F.420, A:V.423, A:V.423, A:I.424, A:I.424, A:V.428, B:V.54, B:V.54, B:I.100, B:I.100 Hydrogen bonds: A:Y.288, A:Y.288 Salt bridges: A:H.411, A:R.481 pi-Cation interactions: A:H.333, A:H.419 Metal complexes: A:H.419

1 x CU: COPPER (II) ION(Non-covalent)

CU.7: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: HEO.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.284, A:H.333, A:H.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Cryo-EM structure of cytochrome bo 3 quinol oxidase assembled in peptidiscs reveals an "open" conformation for potential ubiquinone-8 release. Biochim Biophys Acta Bioenerg (2024)

Release Date

2024-04-24

Peptides

Cytochrome bo(3) ubiquinol oxidase subunit 1: A
Cytochrome bo(3) ubiquinol oxidase subunit 2: B
Cytochrome bo(3) ubiquinol oxidase subunit 3: C
Cytochrome bo(3) ubiquinol oxidase subunit 4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bo(3) ubiquinol oxidase subunit 1

Cytochrome bo(3) ubiquinol oxidase subunit 2

Cytochrome bo(3) ubiquinol oxidase subunit 3

Cytochrome bo(3) ubiquinol oxidase subunit 4

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