SMTL ID : 7cuq.1

2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

HEM.1: 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 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:F.73, A:F.73, A:A.76, A:M.110, A:I.111, A:I.417, A:F.420, A:I.424, A:I.424, A:V.429, A:F.468, A:I.505 Hydrogen bonds: A:Q.83, A:F.103, A:W.170, A:R.482 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:F.420, A:F.468 Metal complexes: A:H.106, A:H.421

1 x HEO: HEME O(Non-covalent)

HEO.2: 31 residues within 4Å: Chain A: W.170, W.280, V.287, Y.288, I.291, H.333, H.334, T.352, A.356, T.359, G.360, I.363, F.364, F.391, S.392, G.395, G.398, V.399, L.401, A.402, D.407, L.410, H.411, L.416, H.419, F.420, V.423, I.424, R.481 Chain B: V.30, A.34 26 PLIP interactions: 24 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:I.291, A:H.333, A:T.359, A:I.363, A:I.363, A:F.364, A:F.391, A:F.391, A:V.399, A:L.416, A:F.420, A:F.420, A:V.423, A:V.423, A:I.424, B:V.30, B:A.34 Hydrogen bonds: A:Y.288 Salt bridges: A:H.411, A:R.481 pi-Stacking: A:H.333, A:H.334 Metal complexes: A:H.419

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

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

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

3PE.4: 18 residues within 4Å: Chain A: F.138, P.139, F.140, L.141, L.144, Q.195, I.199, T.202, L.203, F.602, M.621, W.625 Chain C: K.25, G.28, F.29, Y.32 Ligands: 3PE.5, 3PE.9 14 PLIP interactions: 2 interactions with chain C, 12 interactions with chain A Hydrophobic interactions: C:F.29, A:F.138, A:L.141, A:L.144, A:I.199, A:I.199, A:I.199, A:F.602, A:W.625, A:W.625, A:W.625 Salt bridges: C:K.25 Hydrogen bonds: A:F.140, A:L.141 3PE.5: 10 residues within 4Å: Chain A: T.254, L.255, Y.258, L.259, F.602, M.606, H.609, W.611 Ligands: 3PE.4, 3PE.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.254, A:Y.258, A:L.259, A:F.602, A:F.602, A:W.611, A:W.611 3PE.6: 15 residues within 4Å: Chain A: I.62, I.63, L.122, L.125, G.435, M.436, W.440, A.443, F.444, F.446, M.516, I.520, R.523, R.527 Ligands: 3PE.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.62, A:I.63, A:I.63, A:L.122, A:L.125, A:W.440, A:W.440, A:A.443, A:F.444, A:F.446, A:I.520 Hydrogen bonds: A:R.527, A:R.527 Salt bridges: A:R.523, A:R.523, A:R.523 3PE.8: 13 residues within 4Å: Chain A: L.31, Y.43, L.44, W.48, R.56, M.60, I.63, V.67, V.150, A.443, F.444 Ligands: 3PE.6, UQ8.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.31, A:L.31, A:Y.43, A:L.44, A:W.48, A:W.48, A:I.63, A:V.67, A:V.67 Hydrogen bonds: A:Y.43, A:R.56 Salt bridges: A:K.40 3PE.9: 20 residues within 4Å: Chain A: A.251, F.618, I.622, W.625, I.626, K.628, S.629 Chain C: K.25, F.29, Y.32, T.145, L.148, H.149, S.152, W.156, V.159, R.176, F.183 Ligands: 3PE.4, 3PE.5 20 PLIP interactions: 11 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:F.29, C:Y.32, C:L.148, C:L.148, C:W.156, C:W.156, C:V.159, C:F.183, A:A.251, A:F.618, A:I.622, A:W.625, A:W.625, A:W.625, A:I.626 Salt bridges: C:K.25, C:R.176, C:R.176 Hydrogen bonds: A:K.628, A:S.629

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

UQ8.7: 16 residues within 4Å: Chain A: I.16, T.20, I.24, V.67, M.68, R.71, A.74, H.98, Q.101, I.102, A.105, I.154, N.157, V.158, L.160 Ligands: 3PE.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.16, A:I.24, A:V.67, A:R.71, A:A.74, A:I.154, A:N.157, A:L.160, A:L.160 Hydrogen bonds: A:R.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cryo-EM structures of Escherichia coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-08-25

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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