Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase FO region
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8g07
Q-score: 0.571
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 3-[4-(morpholin-4-yl)phenyl]-4-{[(pyridin-2-yl)methyl]amino}cyclobut-3-ene-1,2-dione (349 Da, Ligand)
- Sq31f-bound mycobacterium smegmatis atp synthase fo region (Complex from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase rotational state 1
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8g08
Q-score: 0.485
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 3-[4-(morpholin-4-yl)phenyl]-4-{[(pyridin-2-yl)methyl]amino}cyclobut-3-ene-1,2-dione (349 Da, Ligand)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Sq31f-bound mycobacterium smegmatis atp synthase rotational state 1 (Complex from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase rotational state 2
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8g09
Q-score: 0.462
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Sq31f-bound mycobacterium smegmatis atp synthase rotational state 2 (Complex from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 3-[4-(morpholin-4-yl)phenyl]-4-{[(pyridin-2-yl)methyl]amino}cyclobut-3-ene-1,2-dione (349 Da, Ligand)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase rotational state 3
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8g0a
Q-score: 0.458
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 3-[4-(morpholin-4-yl)phenyl]-4-{[(pyridin-2-yl)methyl]amino}cyclobut-3-ene-1,2-dione (349 Da, Ligand)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Sq31f-bound mycobacterium smegmatis atp synthase rotational state 3 (Complex from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase FO region
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8g0b
Q-score: 0.578
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (1r,2s)-1-(6-bromo-2-methoxyquinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2,3,6-trimethoxypyridin-4-yl)butan-2-ol (657 Da, Ligand)
- Tbaj-876-bound mycobacterium smegmatis atp synthase fo region (Complex from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 1
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8g0c
Q-score: 0.485
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (1r,2s)-1-(6-bromo-2-methoxyquinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2,3,6-trimethoxypyridin-4-yl)butan-2-ol (657 Da, Ligand)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Tbaj-876-bound mycobacterium smegmatis atp synthase rotational state 1 (Complex from Mycolicibacterium smegmatis MC2 155)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8g0d
Q-score: 0.458
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Tbaj-876-bound mycobacterium smegmatis atp synthase rotational state 2 (Complex from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (1r,2s)-1-(6-bromo-2-methoxyquinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2,3,6-trimethoxypyridin-4-yl)butan-2-ol (657 Da, Ligand)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 3
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8g0e
Q-score: 0.477
Courbon GM, Palme PR, Mann L, Richter A, Imming P, Rubinstein JL
EMBO J (2023) 42 pp. e113687-e113687 [ DOI: doi:10.15252/embj.2023113687 Pubmed: 37377118 ]
- Tbaj-876-bound mycobacterium smegmatis atp synthase rotational state 3 (Complex from Mycolicibacterium smegmatis MC2 155)
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit b (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit b-delta (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit alpha (58 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit c (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (1r,2s)-1-(6-bromo-2-methoxyquinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2,3,6-trimethoxypyridin-4-yl)butan-2-ol (657 Da, Ligand)
- Atp synthase gamma chain (33 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit beta (51 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atp synthase epsilon chain (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Atp synthase subunit a (27 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 [ DOI: doi:10.7554/eLife.71959 Pubmed: 34590581 ]
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 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))
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Copper (ii) ion (63 Da, Ligand)
- Heme c (618 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)
- Lpqe protein (16 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))
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome c oxidase subunit 1 (63 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Menaquinone-9 (785 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Heme-a (852 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 (42 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))
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Respiratory supercomplex ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cardiolipin (1 kDa, Ligand)
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 [ DOI: doi:10.7554/eLife.71959 Pubmed: 34590581 ]
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 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))
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Copper (ii) ion (63 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)
- Heme c (618 Da, Ligand)
- Lpqe protein (16 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))
- Respiratory complex ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Menaquinone-9 (785 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Heme-a (852 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 (42 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))
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome aa3 subunit 2 (35 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome c oxidase subunit 1 (61 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cardiolipin (1 kDa, Ligand)