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 ]
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli BL21(DE3))
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli BL21(DE3))
- 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))
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bo3 quinol oxidase (144 kDa, Complex from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Heme o (838 Da, Ligand)
Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8aw5
Q-score: 0.555
To Be Published
- Heme o oxygenase (34 kDa, Protein from Aquifex aeolicus VF5)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme a synthase with cofactor heme b (Complex from Aquifex aeolicus VF5)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
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)
- 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)
- Copper (ii) ion (63 Da, Ligand)
- Ubiquinol oxidase (22 kDa, Protein from Escherichia coli K-12)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli K-12)
- Ubiquinone-8 (727 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Purified escherichia coli cytochrome bo3 (Complex from Escherichia coli K-12)
- Heme o (838 Da, Ligand)
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 [ Pubmed: 36481732 DOI: doi:10.1038/s41467-022-34771-y ]
- Cytochrome bo3 ubiquinol oxidase (144 kDa, Complex from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Unknown atom or ion (744 Da, Ligand)
- Ubiquinol oxidase subunit 2 (36 kDa, Protein from Escherichia coli)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Heme o (838 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
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 [ Pubmed: 36481732 DOI: doi:10.1038/s41467-022-34771-y ]
- Cytochrome bo3 ubiquinol oxidase (144 kDa, Complex from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Methyl 3-oxidanyl-5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-1-benzothiophene-2-carboxylate (253 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Ubiquinol oxidase subunit 2 (36 kDa, Protein from Escherichia coli)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Unknown atom or ion (Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Heme o (838 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
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)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (10 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (73 kDa, Protein from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- 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 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)
- 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 3 (20 kDa, Protein from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- E. coli cytochrome bo3 ubiquinol oxidase dimer (Complex from Escherichia coli)
- Heme o (838 Da, Ligand)
- 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 [ DOI: doi:10.1073/pnas.2106750118 Pubmed: 34417297 ]
- Water (18 Da, Ligand)
- Ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Zinc ion (65 Da, Ligand)
- Cytochrome o ubiquinol oxidase, subunit i (74 kDa, Protein from Escherichia coli)
- Cytochrome o ubiquinol oxidase (22 kDa, Protein from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Cytochrome bo 3 ubiquinol oxidase (Complex from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome o ubiquinol oxidase, subunit iv (12 kDa, Protein from Escherichia coli)
- Heme o (838 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 [ DOI: doi:10.1073/pnas.2106750118 Pubmed: 34417297 ]
- Heme o (838 Da, Ligand)
- Water (18 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)
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 [ DOI: doi:10.1073/pnas.2106750118 Pubmed: 34417297 ]
- Heme o (838 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase (140 kDa, Complex from Escherichia coli)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli)