Mycobacterial respiratory complex I with both quinone positions modelled
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8e9g
Q-score: 0.537
Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL
PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterial respiratory complex i, consensus map (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- (2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterial respiratory complex I, fully-inserted quinone
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8e9h
Q-score: 0.533
Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL
PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- (2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Mycobacterial respiratory complex i, fully-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterial respiratory complex I, semi-inserted quinone
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8e9i
Q-score: 0.509
Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL
PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- (2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterial respiratory complex i, semi-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 1
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7jg5
Q-score: 0.423
Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL
Nature (2021) 589 pp. 143-147 [ Pubmed: 33299175 DOI: doi:10.1038/s41586-020-3004-3 ]
- Phosphate ion (94 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha,atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 2
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7jg6
Q-score: 0.377
Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL
Nature (2021) 589 pp. 143-147 [ Pubmed: 33299175 DOI: doi:10.1038/s41586-020-3004-3 ]
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 3
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7jg7
Q-score: 0.409
Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL
Nature (2021) 589 pp. 143-147 [ Pubmed: 33299175 DOI: doi:10.1038/s41586-020-3004-3 ]
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of bedaquiline-saturated Mycobacterium smegmatis ATP synthase rotational state 1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7jg8
Q-score: 0.417
Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL
Nature (2021) 589 pp. 143-147 [ Pubmed: 33299175 DOI: doi:10.1038/s41586-020-3004-3 ]
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis)
- Bedaquiline (555 Da, Ligand)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of bedaquiline-saturated Mycobacterium smegmatis ATP synthase rotational state 2
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7jg9
Q-score: 0.387
Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL
Nature (2021) 589 pp. 143-147 [ Pubmed: 33299175 DOI: doi:10.1038/s41586-020-3004-3 ]
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis)
- Bedaquiline (555 Da, Ligand)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of bedaquiline-saturated Mycobacterium smegmatis ATP synthase rotational state 3
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7jga
Q-score: 0.438
Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL
Nature (2021) 589 pp. 143-147 [ Pubmed: 33299175 DOI: doi:10.1038/s41586-020-3004-3 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis)
- Bedaquiline (555 Da, Ligand)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis)
Cryo-EM structure of bedaquiline-washed Mycobacterium smegmatis ATP synthase rotational state 1
Guo H, Courbon GM, Bueler SA, Mai J, Liu J, Rubinstein JL
Nature (2021) 589 pp. 143-147 [ Pubmed: 33299175 DOI: doi:10.1038/s41586-020-3004-3 ]