Kishikawa J, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 [ Pubmed: 35882843 DOI: 10.1038/s41467-022-31718-1 ]
Image sets:
Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xk3
Q-score: 0.567
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Calcium ion (40 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 1 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 2
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xk4
Q-score: 0.562
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Calcium ion (40 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 2 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 3
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xk5
Q-score: 0.546
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 3 (220 kDa, Complex from Vibrio cholerae O395)
- Calcium ion (40 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7xk6
Q-score: 0.575
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Aurachin d (363 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, with aurachin d-42 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7xk7
Q-score: 0.584
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Korormicin (433 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, with korormicin (220 kDa, Complex from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
Grba DN, Blaza JN, Bridges HR, Agip AA, Yin Z, Murai M, Miyoshi H, Hirst J
J Biol Chem (2022) 298 [ Pubmed: 35063503 DOI: 10.1016/j.jbc.2022.101602 ]
Image sets:
The acetogenin-bound complex I of Mus musculus resolved to 3.4 angstroms
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7psa
Q-score: 0.516
Grba DN, Blaza JN, Bridges HR, Agip AA, Yin Z, Murai M, Miyoshi H, Hirst J
J Biol Chem (2022) 298 pp. 101602-101602 [ Pubmed: 35063503 DOI: doi:10.1016/j.jbc.2022.101602 ]
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (30 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (42 kDa, Protein from Mouse)
- Acyl carrier protein, mitochondrial (17 kDa, Protein from Mouse)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (52 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 4l (10 kDa, Protein from house mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (13 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (20 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 (6 kDa, Protein from Mouse)
- Cardiolipin (1 kDa, Ligand)
- Mitochondrial nadh:ubiquinone oxidoreductase from mus musculus (Complex from Mus musculus)
- Nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (50 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 5 (12 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (11 kDa, Protein from Mouse)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (24 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 6 (18 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (16 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial (13 kDa, Protein from Mouse)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (16 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (15 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 1 (36 kDa, Protein from house mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (15 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (17 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial (11 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 subunit c1, mitochondrial (8 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (24 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (19 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 2 (38 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial (21 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 5 (68 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (27 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (15 kDa, Protein from Mouse)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial (40 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (22 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (21 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (21 kDa, Protein from Mouse)
- Zinc ion (65 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (11 kDa, Protein from Mouse)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 subunit c2 (14 kDa, Protein from house mouse)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (79 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (10 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (9 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (8 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (15 kDa, Protein from Mouse)
- ~{s}-[2-[3-[[(2~{r})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{s})-3-oxidanyltetradecanethioate (584 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial (17 kDa, Protein from Mouse)
- Iron/sulfur cluster (351 Da, Ligand)
- (3~{s},5~{s})-5-methyl-3-[(13~{r})-13-oxidanyl-13-[(2~{r},5~{r})-5-[(2~{r},5~{r})-5-[(1~{r})-1-oxidanylundecyl]oxolan-2-yl]oxolan-2-yl]tridecyl]oxolan-2-one (608 Da, Ligand)
- Nadh-ubiquinone oxidoreductase chain 3 (13 kDa, Protein from house mouse)
- Nadh-ubiquinone oxidoreductase chain 4 (51 kDa, Protein from house mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (12 kDa, Protein from Mouse)
Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 6rko
Q-score: 0.665
Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kuhlbrandt W, Michel H
Science (2019) 366 pp. 100-104 [ Pubmed: 31604309 DOI: doi:10.1126/science.aay0967 ]
- Ubiquinone-8 (727 Da, Ligand)
- Cis-heme d hydroxychlorin gamma-spirolactone (632 Da, Ligand)
- Uncharacterized protein ynhf (2 kDa, Protein from Escherichia coli (strain K12))
- Cytochrome bd-i oxidase from e. coli (107 kDa, Complex from Escherichia coli K-12)
- Cytochrome bd-i ubiquinol oxidase subunit 1 (58 kDa, Protein from Escherichia coli (strain K12))
- Cytochrome bd-i ubiquinol oxidase subunit x (4 kDa, Protein from Escherichia coli (strain K12))
- Cytochrome bd-i ubiquinol oxidase subunit 2 (42 kDa, Protein from Escherichia coli (strain K12))
- Heme b/c (618 Da, Ligand)
- Water (18 Da, Ligand)
- Oxygen molecule (31 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)