SMTL ID : 6wti.1

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

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: 22 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 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.73, A:A.76, A:M.110, A:I.111, A:I.111, A:I.417, A:I.424, A:I.425, A:V.429, A:F.468 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, I.355, A.356, T.359, G.360, F.391, 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, V.55, I.100 Ligands: CU.3 22 PLIP interactions: 4 interactions with chain B, 18 interactions with chain A, Hydrophobic interactions: B:V.54, B:V.54, B:V.55, B:I.100, A:W.280, A:V.287, A:I.291, A:A.356, A:V.399, A:A.402, A:L.416, A:F.420, A:F.420, A:F.420, A:I.424, A:V.428 Hydrogen bonds: A:Y.288, A:Y.288 Salt bridges: A:H.411, A:R.481 pi-Cation interactions: A:H.333 Metal complexes: A:H.419

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

CU.3: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: HEO.2 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: 18 residues within 4Å: Chain A: V.10, F.12, I.16, V.17, T.20, I.21, I.24, L.70, R.71, A.74, D.75, M.78, H.98, Q.101, I.102, N.157, L.160, G.161 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.10, A:F.12, A:T.20, A:I.21, A:I.21, A:I.24, A:L.70, A:R.71, A:A.74, A:L.160 Hydrogen bonds: A:R.71, A:R.71

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

3PE.5: 19 residues within 4Å: Chain A: F.138, P.139, F.140, L.141, L.144, F.148, Q.195, I.199, F.602, F.618, M.621, W.625, K.628, V.634 Chain C: K.25, G.28, F.29, Y.32 Ligands: 3PE.11 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.138, A:L.141, A:L.144, A:F.148, A:Q.195, A:I.199, A:I.199, A:F.602, A:W.625, A:W.625, A:W.625, C:Y.32 Hydrogen bonds: A:F.140, A:L.141 Salt bridges: C:K.25, C:K.25 3PE.6: 8 residues within 4Å: Chain A: A.251, T.254, Y.258, F.602, M.606, W.611, I.615 Ligands: 3PE.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.251, A:T.254, A:Y.258, A:F.602, A:W.611, A:W.611, A:W.611, A:W.611, A:I.615 3PE.7: 1 residues within 4Å: Ligands: 3PE.6 No protein-ligand interaction detected (PLIP) 3PE.9: 5 residues within 4Å: Chain A: Y.517, I.520, R.521, R.523 Ligands: U9V.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.517, A:I.520 Salt bridges: A:R.523 3PE.10: 5 residues within 4Å: Chain A: I.350, I.354 Chain B: I.101, A.104, W.108 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.101, B:A.104, A:I.350, A:I.354 3PE.11: 17 residues within 4Å: Chain A: V.248, A.251, F.618, W.625, S.629 Chain C: K.25, F.29, Y.32, L.39, T.145, H.149, S.152, W.156, T.172, R.176, F.183 Ligands: 3PE.5 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:F.29, C:L.39, C:T.145, C:W.156, C:W.156, C:F.183, A:V.248, A:A.251, A:F.618, A:W.625, A:W.625 Salt bridges: C:K.25, C:R.176, C:R.176 Hydrogen bonds: A:W.625 3PE.12: 10 residues within 4Å: Chain C: F.120, H.121, I.124, V.125, P.130, F.140, A.141, G.144, T.145, L.148 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.120, C:H.121, C:I.124, C:P.130, C:L.148 Salt bridges: C:H.121 3PE.13: 9 residues within 4Å: Chain C: C.37, S.41, F.44, A.48, M.201 Chain D: V.85, I.88, A.89, V.93 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.44, C:A.48, D:V.85, D:I.88 3PE.14: 7 residues within 4Å: Chain A: F.209, M.222, W.230, I.240 Chain D: W.76, A.80, F.83 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.209, A:F.209, A:W.230, A:I.240, D:W.76, D:F.83, D:F.83

1 x U9V: pentadecyl(tetradecyl)peroxyanhydride(Non-covalent)

U9V.8: 16 residues within 4Å: Chain A: Y.43, L.44, W.48, M.60, I.62, I.63, I.66, L.125, V.150, M.436, W.439, W.440, F.444, F.446, R.523 Ligands: 3PE.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.44, A:W.48, A:W.48, A:I.62, A:I.62, A:I.63, A:I.66, A:L.125, A:V.150, A:M.436, A:W.440, A:W.440, A:F.444, A:F.444, A:F.444 Hydrogen bonds: A:Y.43 Salt bridges: A:R.523

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, C.C. et al., A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Nat.Methods (2021)

Release Date

2021-01-20

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
A

B
B

C
C

D
D

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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