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)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Unknown atom or ion (744 Da, Ligand)
- Heme o (838 Da, Ligand)
- Ubiquinol oxidase subunit 2 (36 kDa, Protein from Escherichia coli)
- 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 [ 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)
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 ]
- Copper (ii) ion (63 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)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- Heme o (838 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
- 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)
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 ]
- Copper (ii) ion (63 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)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli)
- Heme o (838 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (32 kDa, Protein from Escherichia coli)
- 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)