SMTL ID : 7n9z.1

E. coli cytochrome bo3 in MSP nanodisc

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.19 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.1: 29 residues within 4Å: Chain A: L.7, V.10, F.12, I.16, V.17, M.18, T.20, I.21, A.22, I.24, I.25, V.67, M.68, L.70, R.71, A.74, D.75, M.78, Q.101, I.102, A.105, V.153, I.154, N.157, V.158, L.160, G.161, V.162 Ligands: LHG.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.16, A:T.20, A:I.21, A:I.24, A:I.25, A:L.70, A:A.74, A:N.157, A:V.158 Hydrogen bonds: A:R.71, A:R.71

9 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.2: 19 residues within 4Å: Chain A: L.31, I.35, K.40, Y.43, L.44, W.48, L.49, R.56, I.59, M.60, I.63, V.64, V.67, F.146, W.147, V.150, F.444 Ligands: LHG.3, LHG.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.35, A:Y.43, A:L.44, A:W.48, A:I.63, A:I.63, A:V.64 Hydrogen bonds: A:Y.43, A:Y.43 LHG.3: 18 residues within 4Å: Chain A: I.59, I.62, I.63, I.66, L.122, L.125, G.435, M.436, W.439, W.440, A.443, F.444, F.446, M.516, I.520, R.523, R.527 Ligands: LHG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.62, A:I.62, A:I.66, A:L.125, A:W.439, A:W.440, A:W.440, A:A.443, A:F.444, A:F.444, A:F.444, A:F.446, A:I.520 Salt bridges: A:R.523, A:R.523, A:R.523, A:R.527 LHG.4: 18 residues within 4Å: Chain A: W.41, T.42, W.45, K.46, L.49, W.147, V.150, V.151, I.154, I.593, V.594, A.596, A.597, F.598, T.600, I.601 Ligands: LHG.7, LHG.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.41, A:W.45, A:W.45, A:W.45, A:L.49, A:I.154, A:I.593, A:V.594, A:A.597, A:F.598, A:I.601 Salt bridges: A:K.46 LHG.5: 26 residues within 4Å: Chain A: F.209, R.216, T.221, M.222, F.223, W.230, L.233, V.237, I.240, A.241, W.318, V.321, C.322, V.325, L.326 Chain C: I.31, M.34, I.38 Chain D: E.74, G.75, W.76, T.79, A.80, F.83, T.84 Ligands: CDL.12 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:F.209, A:F.223, A:W.230, A:I.240, A:W.318, A:V.321, A:V.325, A:L.326, D:T.79, D:F.83, D:F.83, D:F.83 Hydrogen bonds: A:R.216, A:M.222 LHG.6: 18 residues within 4Å: Chain A: W.192, Q.195, I.199, T.247, A.251, T.254, L.255, Y.258, L.259, F.602, M.606, W.611, A.614, I.615, F.618 Ligands: 3PE.9, LHG.16, 3PE.17 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.192, A:A.251, A:T.254, A:Y.258, A:L.259, A:F.602, A:W.611, A:W.611, A:W.611, A:F.618 Hydrogen bonds: A:W.611 LHG.7: 19 residues within 4Å: Chain A: W.45, N.588, S.589, G.590, A.591, V.594, F.598, W.612, I.615, V.616, A.619, G.620, I.623, T.624, V.627, K.628, D.631 Ligands: LHG.4, LHG.15 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.598, A:I.615, A:V.616, A:T.624 Hydrogen bonds: A:N.588, A:S.589, A:G.590, A:K.628, A:D.631, A:D.631 LHG.8: 13 residues within 4Å: Chain A: G.28, L.31, V.32, I.35, G.39, W.41, T.42, L.44, L.49, I.154 Ligands: UQ8.1, LHG.2, LHG.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.41, A:W.41 Hydrogen bonds: A:G.39, A:W.41, A:T.42 LHG.15: 15 residues within 4Å: Chain A: I.615, F.618, A.619, I.622, I.623, I.626, V.627, F.630 Chain C: W.106, I.155, A.158, V.159, V.162, R.167 Ligands: LHG.7 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:W.106, C:A.158, C:V.159, A:A.619, A:I.623, A:V.627, A:F.630, A:F.630 Hydrogen bonds: C:R.167 Salt bridges: C:R.167 LHG.16: 19 residues within 4Å: Chain A: A.251, L.255, L.259 Chain C: I.113, I.117, F.120, H.121, I.124, V.125, P.130, F.140, A.141, G.144, T.145, G.147, L.148, T.151 Ligands: LHG.6, 3PE.17 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.117, C:F.120, C:L.148, C:T.151, A:L.255, A:L.259

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

3PE.9: 28 residues within 4Å: Chain A: F.138, P.139, F.140, L.141, L.144, F.148, W.192, L.196, I.199, L.203, I.206, T.247, I.595, F.602, F.618, M.621, I.622, W.625, K.628, V.634 Chain C: K.25, G.28, F.29, Y.32, R.176, C.179 Ligands: LHG.6, 3PE.17 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain A Hydrophobic interactions: C:Y.32, C:Y.32, A:F.138, A:L.141, A:L.144, A:F.148, A:W.192, A:I.199, A:L.203, 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 3PE.17: 32 residues within 4Å: Chain A: T.247, V.248, A.251, L.252, F.618, I.622, W.625, I.626, K.628, S.629 Chain C: K.25, F.29, Y.32, L.39, L.43, A.141, T.145, L.148, H.149, T.151, S.152, I.155, W.156, V.159, T.172, T.175, R.176, C.179, F.183 Ligands: LHG.6, 3PE.9, LHG.16 25 PLIP interactions: 15 interactions with chain C, 10 interactions with chain A Hydrophobic interactions: C:F.29, C:L.43, C:L.43, C:T.145, C:L.148, C:I.155, C:I.155, C:W.156, C:W.156, A:V.248, A:A.251, A:F.618, A:I.622, A:I.622, A:W.625, A:W.625, A:W.625, A:W.625 Hydrogen bonds: C:W.156, A:W.625 Water bridges: C:K.25, C:R.176 Salt bridges: C:K.25, C:R.176, C:R.176

1 x HEO: HEME O(Non-covalent)

HEO.10: 45 residues within 4Å: Chain A: I.111, W.170, W.280, V.287, Y.288, L.290, I.291, H.333, H.334, F.336, T.352, M.353, I.355, A.356, I.357, T.359, G.360, I.363, F.364, F.391, S.392, G.395, M.396, G.398, V.399, L.401, A.402, D.407, H.411, N.412, L.416, H.419, F.420, V.423, I.424, V.428, R.481 Chain B: M.51, V.54, V.55, A.58, P.96, I.99, I.100 Ligands: HEM.11 34 PLIP interactions: 29 interactions with chain A, 4 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:I.291, A:H.333, A:T.352, A:A.356, A:T.359, A:I.363, A:F.364, A:F.391, A:L.401, A:F.420, A:F.420, A:V.423, A:I.424, B:V.54, B:V.55, B:P.96, B:I.100 Hydrogen bonds: A:W.170, A:Y.288, A:D.407, A:N.412 Water bridges: A:W.280, A:T.359, A:R.481, A:R.482 Salt bridges: A:H.411, A:R.481 pi-Cation interactions: A:H.284, A:H.333 Metal complexes: A:H.419, H2O.4

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

HEM.11: 33 residues within 4Å: Chain A: L.69, F.73, A.76, M.79, R.80, Q.83, F.103, T.104, H.106, G.107, M.110, I.111, A.115, G.169, W.170, L.290, L.414, I.417, F.420, H.421, I.424, I.425, V.429, W.460, A.467, F.468, L.471, R.481, R.482, A.502, I.505, I.509 Ligands: HEO.10 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:F.73, A:A.76, A:M.110, A:I.111, A:A.115, A:I.417, A:F.420, A:I.424, A:I.424, A:V.429, A:W.460, A:F.468 Hydrogen bonds: A:Q.83, A:W.170, A:R.482 Water bridges: A:R.482, A:L.483 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:F.420, A:H.421, A:F.468 pi-Cation interactions: A:H.106 Metal complexes: A:H.106, A:H.421

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 16 residues within 4Å: Chain A: F.223, T.314, S.315, W.318, C.322, V.325, R.561 Chain B: H.84, N.86, E.89, A.90, W.93, T.94, I.97 Chain D: L.86 Ligands: LHG.5 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.314, A:W.318, A:W.318, B:W.93, B:W.93, B:W.93, B:W.93, B:I.97 Hydrogen bonds: A:T.314, A:W.318 Water bridges: A:T.314, A:S.315 Salt bridges: A:R.561

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

CU.13: 3 residues within 4Å: Chain A: H.284, H.333, H.334 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.284, A:H.333, A:H.334, H2O.4

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain A: M.273 Chain B: M.186, M.189 Chain D: M.106 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-09-01

Peptides

Cytochrome o ubiquinol oxidase, subunit I: A
Ubiquinol oxidase subunit 2: B
Cytochrome o ubiquinol oxidase: C
Cytochrome o ubiquinol oxidase, subunit IV: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

Membrane

We predict this structure to be a membrane protein.
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Cytochrome o ubiquinol oxidase, subunit I

Ubiquinol oxidase subunit 2

Cytochrome o ubiquinol oxidase

Cytochrome o ubiquinol oxidase, subunit IV

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