Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 8j0s
Q-score: 0.592
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ DOI: doi:10.1038/s41586-024-07605-8 Pubmed: 38961288 ]
- Atp synthase epsilon chain (13 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit b (18 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit c (8 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase gamma chain (33 kDa, Protein from Mycobacterium tuberculosis)
- Bedaquiline (555 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Mycobacterium tuberculosis atp synthase in complex with bedaquiline(bdq) (Complex from Mycobacterium tuberculosis)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit beta (53 kDa, Protein from Mycobacterium tuberculosis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit a (27 kDa, Protein from Mycobacterium tuberculosis)
- Multifunctional fusion protein (48 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit alpha (59 kDa, Protein from Mycobacterium tuberculosis)
Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in the apo-form
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8j0t
Q-score: 0.543
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ DOI: doi:10.1038/s41586-024-07605-8 Pubmed: 38961288 ]
- Atp synthase epsilon chain (13 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit b (18 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit c (8 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase gamma chain (33 kDa, Protein from Mycobacterium tuberculosis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit beta (53 kDa, Protein from Mycobacterium tuberculosis)
- Mycobacterium tuberculosis atp synthase (Complex from Mycobacterium tuberculosis)
- Atp synthase subunit a (27 kDa, Protein from Mycobacterium tuberculosis)
- Multifunctional fusion protein (48 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit alpha (59 kDa, Protein from Mycobacterium tuberculosis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Cryo-EM structure of Mycobacterium tuberculosis ATP synthase Fo in complex with bedaquiline(BDQ)
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8j57
Q-score: 0.574
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ DOI: doi:10.1038/s41586-024-07605-8 Pubmed: 38961288 ]
- Atp synthase subunit a (27 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit c (8 kDa, Protein from Mycobacterium tuberculosis)
- Bedaquiline (555 Da, Ligand)
- Mycobacterium tuberculosis atp synthase fo with bedaquiline(bdq) (Complex from Mycobacterium tuberculosis)
Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8jr0
Q-score: 0.545
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ DOI: doi:10.1038/s41586-024-07605-8 Pubmed: 38961288 ]
- Atp synthase epsilon chain (13 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit b (18 kDa, Protein from Mycobacterium tuberculosis)
- (1~{s},2~{s})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol (614 Da, Ligand)
- Atp synthase subunit c (8 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase gamma chain (33 kDa, Protein from Mycobacterium tuberculosis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit beta (53 kDa, Protein from Mycobacterium tuberculosis)
- Mycobacterium tuberculosis atp synthase (Complex from Mycobacterium tuberculosis)
- Atp synthase subunit a (27 kDa, Protein from Mycobacterium tuberculosis)
- Multifunctional fusion protein (48 kDa, Protein from Mycobacterium tuberculosis)
- Atp synthase subunit alpha (59 kDa, Protein from Mycobacterium tuberculosis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Structure of the human ATP synthase bound to bedaquiline (membrane domain)
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8khf
Q-score: 0.508
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ DOI: doi:10.1038/s41586-024-07605-8 Pubmed: 38961288 ]
- Atp synthase subunit f, mitochondrial (10 kDa, Protein from Homo sapiens)
- Atp synthase subunit a (24 kDa, Protein from Homo sapiens)
- Atp synthase protein 8 (8 kDa, Protein from Homo sapiens)
- Bedaquiline (555 Da, Ligand)
- Atp synthase f(0) complex subunit c1, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase f(0) complex subunit b1, mitochondrial (24 kDa, Protein from Homo sapiens)
- Human atp synthase (Complex from Homo sapiens)
- Atp synthase subunit atp5mj, mitochondrial (6 kDa, Protein from Homo sapiens)
- Atp synthase subunit g, mitochondrial (11 kDa, Protein from Homo sapiens)
- Atp synthase subunit e, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase subunit d, mitochondrial (18 kDa, Protein from Homo sapiens)
- Atp synthase subunit epsilon, mitochondrial (5 kDa, Protein from Homo sapiens)
- Atp synthase subunit gamma, mitochondrial (30 kDa, Protein from Homo sapiens)
- Atp synthase subunit delta, mitochondrial (15 kDa, Protein from Homo sapiens)
Structure of the human ATP synthase bound to bedaquiline (composite)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8ki3
Q-score: 0.547
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ DOI: doi:10.1038/s41586-024-07605-8 Pubmed: 38961288 ]
- Atpase inhibitor, mitochondrial (9 kDa, Protein from Homo sapiens)
- Atp synthase subunit beta, mitochondrial (51 kDa, Protein from Homo sapiens)
- Human atp synthase (Complex from Homo sapiens)
- Atp synthase subunit atp5mj, mitochondrial (6 kDa, Protein from Homo sapiens)
- Atp synthase subunit e, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase subunit d, mitochondrial (18 kDa, Protein from Homo sapiens)
- Atp synthase subunit g, mitochondrial (11 kDa, Protein from Homo sapiens)
- Atp synthase subunit gamma, mitochondrial (30 kDa, Protein from Homo sapiens)
- Atp synthase-coupling factor 6, mitochondrial (12 kDa, Protein from Homo sapiens)
- Atp synthase subunit a (24 kDa, Protein from Homo sapiens)
- Atp synthase f(0) complex subunit c1, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase subunit alpha, mitochondrial (55 kDa, Protein from Homo sapiens)
- Atp synthase subunit o, mitochondrial (20 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit epsilon, mitochondrial (5 kDa, Protein from Homo sapiens)
- Atp synthase subunit f, mitochondrial (10 kDa, Protein from Homo sapiens)
- Atp synthase protein 8 (8 kDa, Protein from Homo sapiens)
- Bedaquiline (555 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Atp synthase f(0) complex subunit b1, mitochondrial (24 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit delta, mitochondrial (15 kDa, Protein from Homo sapiens)
cryo-EM structure of the human respiratory complex II
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8gs8
Q-score: 0.577
Du Z, Zhou X, Lai Y, Xu J, Zhang Y, Zhou S, Feng Z, Yu L, Tang Y, Wang W, Yu L, Tian C, Ran T, Chen H, Guddat LW, Liu F, Gao Y, Rao Z, Gong H
PNAS (2023) 120 pp. e2216713120-e2216713120 [ Pubmed: 37098072 DOI: doi:10.1073/pnas.2216713120 ]
- Succinate dehydrogenase cytochrome b560 subunit, mitochondrial (18 kDa, Protein from Homo sapiens)
- Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial (17 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (31 kDa, Protein from Homo sapiens)
- The human mitochondrial complex ii, composed of sdha, sdhb, sdhc and sdhd (Complex from Homo sapiens)
- Fe3-s4 cluster (295 Da, Ligand)
- (1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (720 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (72 kDa, Protein from Homo sapiens)
- Ubiquinone-1 (250 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
Resolution: 2.67 Å
EM Method: Single-particle
Fitted PDBs: 7e1w
Q-score: 0.569
Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, Rao Z, Gong H
eLife (2021) 10 [ DOI: doi:10.7554/eLife.69418 Pubmed: 34819223 ]
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv in the presence of q203 (800 kDa, Complex from Mycolicibacterium smegmatis MC2 51)
- 6-chloranyl-2-ethyl-n-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide (557 Da, Ligand)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Copper (ii) ion (63 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Water (18 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 7e1x
Q-score: 0.513
Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, Rao Z, Gong H
eLife (2021) 10 [ DOI: doi:10.7554/eLife.69418 Pubmed: 34819223 ]
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Copper (ii) ion (63 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- 5-methoxy-2-methyl-~{n}-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]pyrazolo[1,5-a]pyridine-3-carboxamide (538 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv in presence of tb47 (800 kDa, Complex from Mycolicibacterium smegmatis MC2 51)
- Mycobacterium tuberculosis complexiii (Complex)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 7e1v
Q-score: 0.614
Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, Rao Z, Gong H
eLife (2021) 10 [ DOI: doi:10.7554/eLife.69418 Pubmed: 34819223 ]
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Mycobacterium tuberculosis complexiii (Complex from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Copper (ii) ion (63 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Apo hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv (800 kDa, Complex from Mycolicibacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Mycobacterium smegmatis complexiv (Complex)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)