SMTL ID : 8go3.1

Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent

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: 25 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, A.115, G.169, W.170, L.414, I.417, F.420, H.421, I.424, I.425, V.429, W.460, 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:A.115, A:I.417, A:F.420, A:F.420, A:I.424, A:I.425, A:I.425, A:V.429, A:W.460, A:I.505, 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, 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, R.481 Chain B: M.51, V.54, V.55, A.58, P.96, I.100 21 PLIP interactions: 5 interactions with chain B, 16 interactions with chain A, Hydrophobic interactions: B:V.54, B:V.55, B:A.58, B:P.96, B:I.100, A:W.280, A:V.287, A:I.291, A:H.333, A:V.399, A:L.401, A:F.420, A:F.420, A:V.423, A:I.424 Hydrogen bonds: A:Y.288, A:H.333 Salt bridges: A:H.411, A:R.481 pi-Cation interactions: A:H.284 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

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

UQ8.4: 11 residues within 4Å: Chain A: I.16, T.20, I.24, L.70, R.71, F.73, A.74, D.75, M.78, H.98, V.513 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.20, A:I.24, A:R.71, A:F.73, A:F.73, A:A.74, A:V.513 Hydrogen bonds: A:T.20

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

3PE.5: 17 residues within 4Å: Chain A: F.138, P.139, F.140, L.141, L.144, F.148, Q.195, I.199, L.203, F.602, M.621, W.625, V.634 Chain C: K.25, F.29, Y.32 Ligands: 3PE.6 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.141, A:L.141, A:L.144, A:F.148, A:Q.195, A:I.199, A:I.199, A:I.199, A:L.203, A:F.602, A:W.625, A:W.625, A:W.625, A:W.625, A:W.625, C:F.29, C:Y.32 Hydrogen bonds: A:F.140, A:L.141 Salt bridges: C:K.25 3PE.6: 16 residues within 4Å: Chain A: A.251, I.622, W.625, I.626, S.629 Chain C: K.25, F.29, Y.32, T.145, H.149, S.152, I.155, W.156, V.159, R.176 Ligands: 3PE.5 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:F.29, C:I.155, C:W.156, C:W.156, C:V.159, A:A.251, A:I.622, 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:W.625, A:S.629

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H.Y. et al., Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent. To Be Published

Release Date

2023-08-30

Peptides

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

ubiquinol oxidase

Cytochrome bo(3) ubiquinol oxidase subunit 4

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