1 ATP-bound V1EG of V/A-ATPase from Thermus thermophilus
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8gxu
Q-score: 0.582
Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K
J Biol Chem (2023) 299 pp. 102884-102884 [ DOI: doi:10.1016/j.jbc.2023.102884 Pubmed: 36626983 ]
- V-type atp synthase, subunit (vapc-therm) (13 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
- Sulfate ion (96 Da, Ligand)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- 1 atp-bound v1eg of v/a-atpase from thermus thermophilus (600 kDa, Complex from Thermus thermophilus HB8)
- Adenosine-5'-triphosphate (507 Da, Ligand)
2 ATP-bound V1EG of V/A-ATPase from Thermus thermophilus
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8gxw
Q-score: 0.539
Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K
J Biol Chem (2023) 299 pp. 102884-102884 [ Pubmed: 36626983 DOI: doi:10.1016/j.jbc.2023.102884 ]
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 2 atp-bound v1eg of v/a-atpase from thermus thermophilus (600 kDa, Complex from Thermus thermophilus HB8)
- Sulfate ion (96 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase, subunit (vapc-therm) (13 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
3 nucleotide-bound V1EG of V/A-ATPase from Thermus thermophilus.
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8gxx
Q-score: 0.506
Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K
J Biol Chem (2023) 299 pp. 102884-102884 [ Pubmed: 36626983 DOI: doi:10.1016/j.jbc.2023.102884 ]
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 3 nucleotide-bound v1eg of v/a-atpase from thermus thermophilus. (600 kDa, Complex from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase, subunit (vapc-therm) (13 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
2 sulfate-bound V1EG of V/A-ATPase from Thermus thermophilus.
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8gxy
Q-score: 0.56
Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K
J Biol Chem (2023) 299 pp. 102884-102884 [ DOI: doi:10.1016/j.jbc.2023.102884 Pubmed: 36626983 ]
- V-type atp synthase, subunit (vapc-therm) (13 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
- Sulfate ion (96 Da, Ligand)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- 2 sulfate-bound v1eg of v/a-atpase from thermus thermophilus. (600 kDa, Complex from Thermus thermophilus HB8)
1 sulfate and 1 ATP bound V1EG of V/A-ATPase from Thermus thermophilus.
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8gxz
Q-score: 0.488
Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K
J Biol Chem (2023) 299 pp. 102884-102884 [ Pubmed: 36626983 DOI: doi:10.1016/j.jbc.2023.102884 ]
- 1 sulfate and 1 atp bound v1eg of v/a-atpase from thermus thermophilus (600 kDa, Complex from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Sulfate ion (96 Da, Ligand)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase, subunit (vapc-therm) (13 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
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 ]
- Riboflavin (376 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 1 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 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 ]
- Riboflavin (376 Da, Ligand)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 2 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 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 ]
- Riboflavin (376 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 3 (220 kDa, Complex from Vibrio cholerae O395)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 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 c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Water (18 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Riboflavin (376 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Aurachin d (363 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, with aurachin d-42 (220 kDa, Complex from Vibrio cholerae O395)
- Calcium ion (40 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 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 ]
- Riboflavin (376 Da, Ligand)
- Korormicin (433 Da, Ligand)
- Water (18 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, with korormicin (220 kDa, Complex from Vibrio cholerae O395)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)