Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8qqk
Q-score: 0.594
Gao Y, Zhang Y, Hakke S, Mohren R, Sijbers LJPM, Peters PJ, Ravelli RBG
Biochim Biophys Acta Bioenerg (2024) 1865 pp. 149045-149045 [ DOI: doi:10.1016/j.bbabio.2024.149045 Pubmed: 38614453 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli BL21(DE3))
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli BL21(DE3))
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Heme o (838 Da, Ligand)
- Cytochrome bo3 quinol oxidase (144 kDa, Complex from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli BL21(DE3))
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli BL21(DE3))
Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 8go3
Q-score: 0.553
To Be Published
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli K-12)
- Ubiquinol oxidase (22 kDa, Protein from Escherichia coli K-12)
- Heme o (838 Da, Ligand)
- Purified escherichia coli cytochrome bo3 (Complex from Escherichia coli K-12)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli K-12)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7xmc
Q-score: 0.526
Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y
Nat Commun (2022) 13 pp. 7591-7591 [ DOI: doi:10.1038/s41467-022-34771-y Pubmed: 36481732 ]
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Cytochrome bo3 ubiquinol oxidase (144 kDa, Complex from Escherichia coli)
- Ubiquinol oxidase subunit 2 (36 kDa, Protein from Escherichia coli)
- Heme o (838 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Unknown atom or ion (744 Da, Ligand)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 7xmd
Q-score: 0.535
Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y
Nat Commun (2022) 13 pp. 7591-7591 [ DOI: doi:10.1038/s41467-022-34771-y Pubmed: 36481732 ]
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Methyl 3-oxidanyl-5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-1-benzothiophene-2-carboxylate (253 Da, Ligand)
- Cytochrome bo3 ubiquinol oxidase (144 kDa, Complex from Escherichia coli)
- Ubiquinol oxidase subunit 2 (36 kDa, Protein from Escherichia coli)
- Heme o (838 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Unknown atom or ion (Ligand)
E. coli cytochrome bo3 ubiquinol oxidase monomer
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8f68
Q-score: 0.506
Guo Y, Karimullina E, Emde T, Otwinowski Z, Borek D, Savchenko A
Protein Sci (2023) 32 pp. e4616-e4616 [ Pubmed: 36880269 DOI: doi:10.1002/pro.4616 ]
- E. coli cytochrome bo3 ubiquinol oxidase monomer (Complex from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (73 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (20 kDa, Protein from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Heme o (838 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (10 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (28 kDa, Protein from Escherichia coli)
E. coli cytochrome bo3 ubiquinol oxidase dimer
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 8f6c
Q-score: 0.429
Guo Y, Karimullina E, Emde T, Otwinowski Z, Borek D, Savchenko A
Protein Sci (2023) 32 pp. e4616-e4616 [ Pubmed: 36880269 DOI: doi:10.1002/pro.4616 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (73 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (20 kDa, Protein from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Heme o (838 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (10 kDa, Protein from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- E. coli cytochrome bo3 ubiquinol oxidase dimer (Complex from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (28 kDa, Protein from Escherichia coli)
E. coli cytochrome bo3 in MSP nanodisc
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 7n9z
Q-score: 0.734
Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R
PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]
- Ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Cytochrome bo 3 ubiquinol oxidase (Complex from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Heme o (838 Da, Ligand)
- Cytochrome o ubiquinol oxidase (22 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Cytochrome o ubiquinol oxidase, subunit iv (12 kDa, Protein from Escherichia coli)
- Cytochrome o ubiquinol oxidase, subunit i (74 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Zinc ion (65 Da, Ligand)
2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 7cub
Q-score: 0.645
Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R
PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Ubiquinone-8 (727 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
- Heme o (838 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Water (18 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 7cuq
Q-score: 0.597
Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R
PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Ubiquinone-8 (727 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
- Heme o (838 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 7cuw
Q-score: 0.63
Li J, Han L, Vallese F, Ding Z, Choi SK, Hong S, Luo Y, Liu B, Chan CK, Tajkhorshid E, Zhu J, Clarke O, Zhang K, Gennis R
PNAS (2021) 118 [ Pubmed: 34417297 DOI: doi:10.1073/pnas.2106750118 ]
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Ubiquinone-8 (727 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
- Heme o (838 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)