Mycobacterial supercomplex malate:quinone oxidoreductase assembly
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dm1
Q-score: 0.38
Di Trani JM, Yu J, Courbon GM, Lobez Rodriguez AP, Cheung J, Liang Y, Coupland CE, Bueler SA, Cook GM, Brzezinski P, Rubinstein J
To Be Published
- Cytochrome c oxidase subunit 1 (63 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Probable malate:quinone oxidoreductase (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (23 kDa, Protein from Mycolicibacterium smegmatis MC2 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)
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex rieske iron-sulfur subunit (42 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Palmitic acid (256 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme-a (852 Da, Ligand)
- Cytochrome aa3 subunit 2 (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Respiratory complex mqo:ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Lpqe protein (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cardiolipin (1 kDa, Ligand)
III2IV respiratory supercomplex from Saccharomyces cerevisiae
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 9etz
Q-score: 0.639
Lobez AP, Wu F, Di Trani JM, Rubinstein JL, Oliveberg M, Brzezinski P, Moe A
Nat Commun (2024) 15 pp. 8241-8241 [ DOI: doi:10.1038/s41467-024-52475-3 Pubmed: 39300056 ]
- Cytochrome c oxidase subunit 12, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b-c1 complex subunit 6, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome b-c1 complex subunit 1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 26, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 8, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae)
- 5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol (592 Da, Ligand)
- Cytochrome c oxidase subunit 7, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- Heme c (618 Da, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Cytochrome c1, heme protein, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 8, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Water (18 Da, Ligand)
- Cytochrome c oxidase subunit 2 (26 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 6, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Heme-a (852 Da, Ligand)
- Cytochrome c oxidase subunit 3 (30 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 13, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 1 (58 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Iii2-iv respiratory supercomplex (Complex from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 4, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 2, mitochondrial (38 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 5a, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phoshocholine (734 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b-c1 complex subunit 10, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 7, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome b (43 kDa, Protein from Saccharomyces cerevisiae)
cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8smr
Q-score: 0.608
Di Trani JM, Gheorghita AA, Turner M, Brzezinski P, Adelroth P, Vahidi S, Howell PL, Rubinstein JL
PNAS (2023) 120 pp. e2307093120-e2307093120 [ DOI: doi:10.1073/pnas.2307093120 Pubmed: 37751552 ]
- Calcium ion (40 Da, Ligand)
- Cbb3-type cytochrome c oxidase subunit (34 kDa, Protein from Pseudomonas aeruginosa)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c5 (13 kDa, Protein from Pseudomonas aeruginosa)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cbb3-type cytochrome c oxidase subunit ii (22 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome b (46 kDa, Protein from Pseudomonas aeruginosa)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome c4 (18 kDa, Protein from Pseudomonas aeruginosa)
- Ubiquinone-10 (863 Da, Ligand)
- Cytochrome-c oxidase (52 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome bc1-cbb3 supercomplex (374 MDa, Complex from Pseudomonas aeruginosa)
- (2r)-2-(methoxymethyl)-4-{[(25r)-spirost-5-en-3beta-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-beta-d-glucopyranoside (855 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome c1 (26 kDa, Protein from Pseudomonas aeruginosa)
cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8snh
Q-score: 0.613
Di Trani JM, Gheorghita AA, Turner M, Brzezinski P, Adelroth P, Vahidi S, Howell PL, Rubinstein JL
PNAS (2023) 120 pp. e2307093120-e2307093120 [ DOI: doi:10.1073/pnas.2307093120 Pubmed: 37751552 ]
- Calcium ion (40 Da, Ligand)
- Cbb3-type cytochrome c oxidase subunit (33 kDa, Protein from Pseudomonas aeruginosa)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c5 (13 kDa, Protein from Pseudomonas aeruginosa)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cbb3-type cytochrome c oxidase subunit ii (22 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome b (46 kDa, Protein from Pseudomonas aeruginosa)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome c4 (18 kDa, Protein from Pseudomonas aeruginosa)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome-c oxidase (52 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome bc1-cbb3 supercomplex (374 MDa, Complex from Pseudomonas aeruginosa)
- (2r)-2-(methoxymethyl)-4-{[(25r)-spirost-5-en-3beta-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-beta-d-glucopyranoside (855 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome c1 (26 kDa, Protein from Pseudomonas aeruginosa)
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)