Structure of mycobacterial NDH2 (type II NADH:quinone oxidoreductase)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9mqy
Q-score: 0.558
Liang Y, Bueler SA, Cook GM, Rubinstein JL
To Be Published
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9mqz
Q-score: 0.514
Liang Y, Bueler SA, Cook GM, Rubinstein JL
To Be Published
- Ndh2 (non-electrogenic nadh:quinone oxidoreductase) from mycobacterium smegmatis (49 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- N-cyclohexyl-2-[(4-oxo-1,4-dihydroquinazolin-2-yl)sulfanyl]acetamide (317 Da, Ligand)
- Nadh:ubiquinone reductase (non-electrogenic) (53 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterial CIII2CIV2 supercomplex, Inhibitor free
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7rh5
Q-score: 0.513
Yanofsky DJ, Di Trani JM, Krol S, Abdelaziz R, Bueler SA, Imming P, Brzezinski P, Rubinstein JL
eLife (2021) 10 [ Pubmed: 34590581 DOI: doi:10.7554/eLife.71959 ]
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cardiolipin (1 kDa, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Respiratory supercomplex ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- (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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome bc1 complex cytochrome c subunit (23 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 1 (63 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Putative conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Lpqe protein (16 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (42 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome aa3 subunit 2 (38 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Mycobacterial CIII2CIV2 supercomplex, inhibitor free, -Lpqe cyt cc open
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7rh6
Q-score: 0.395
Yanofsky DJ, Di Trani JM, Krol S, Abdelaziz R, Bueler SA, Imming P, Brzezinski P, Rubinstein JL
eLife (2021) 10 [ Pubmed: 34590581 DOI: doi:10.7554/eLife.71959 ]
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 1 (61 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Menaquinone-9 (785 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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome bc1 complex cytochrome c subunit (23 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cytochrome aa3 subunit 2 (35 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Heme-a (852 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme c (618 Da, Ligand)
- Putative conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Lpqe protein (16 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Respiratory complex ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (42 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Mycobacterial CIII2CIV2 supercomplex, Telacebec (Q203) bound
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7rh7
Q-score: 0.477
Yanofsky DJ, Di Trani JM, Krol S, Abdelaziz R, Bueler SA, Imming P, Brzezinski P, Rubinstein JL
eLife (2021) 10 [ Pubmed: 34590581 DOI: doi:10.7554/eLife.71959 ]
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cardiolipin (1 kDa, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- 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)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Lpqe protein (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome aa3 subunit 2 (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex rieske iron-sulfur subunit (42 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme-a (852 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme c (618 Da, Ligand)
- Respiratory complex ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase subunit 1 (61 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex cytochrome c subunit (23 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)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 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,atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit beta (51 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 alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 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 from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit beta (51 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 alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase epsilon chain (13 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 from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit beta (51 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-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Bedaquiline (555 Da, Ligand)
- Atp synthase epsilon chain (13 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 from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit beta (51 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-delta (47 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis)
- Bedaquiline (555 Da, Ligand)
- Atp synthase epsilon chain (13 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 from mycobacterium smegmatis (550 kDa, Complex from Mycolicibacterium smegmatis)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis)