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)
Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9b8p
Q-score: 0.529
Coupland CE, Karimi R, Bueler SA, Liang Y, Courbon GM, Di Trani JM, Wong CJ, Saghian R, Youn JY, Wang LY, Rubinstein JL
Science (2024) 385 pp. 168-174 [ DOI: doi:10.1126/science.adp5577 Pubmed: 38900912 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- V-type proton atpase subunit g (13 kDa, Protein from Rattus norvegicus)
- Atpase h+-transporting v1 subunit d (28 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Rattus norvegicus)
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, v1 (Complex from Rattus norvegicus)
- V-type proton atpase subunit f (13 kDa, Protein from Rattus norvegicus)
- Sidk (65 kDa, Protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1)
- H(+)-transporting two-sector atpase (71 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Rattus norvegicus)
Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9b8o
Q-score: 0.513
Coupland CE, Karimi R, Bueler SA, Liang Y, Courbon GM, Di Trani JM, Wong CJ, Saghian R, Youn JY, Wang LY, Rubinstein JL
Science (2024) 385 pp. 168-174 [ DOI: doi:10.1126/science.adp5577 Pubmed: 38900912 ]
- V-type proton atpase 116 kda subunit a 1 (94 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Rattus norvegicus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Atpase h+-transporting v1 subunit d (28 kDa, Protein from Rattus norvegicus)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Rattus norvegicus)
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, vo (Complex from Rattus norvegicus)
- Phosphatidylethanolamine (734 Da, Ligand)
- Synaptophysin (33 kDa, Protein from Rattus norvegicus)
- Renin receptor (39 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit (40 kDa, Protein from Rattus norvegicus)
- Rnasek protein (9 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit f (13 kDa, Protein from Rattus norvegicus)
- Methyl (3r,6z,10e,14e)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate (534 Da, Ligand)
- (7r)-4,7-dihydroxy-n,n,n-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacosan-1-aminium 4-oxide (524 Da, Ligand)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Rattus norvegicus)
- Cholesterol (386 Da, Ligand)
- Atpase, h+ transporting, v0 subunit b (predicted), isoform cra_a (21 kDa, Protein from Rattus norvegicus)
Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9b8q
Q-score: 0.363
Coupland CE, Karimi R, Bueler SA, Liang Y, Courbon GM, Di Trani JM, Wong CJ, Saghian R, Youn JY, Wang LY, Rubinstein JL
Science (2024) 385 pp. 168-174 [ DOI: doi:10.1126/science.adp5577 Pubmed: 38900912 ]
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, peripheral stalks (Complex from Rattus norvegicus)
- V-type proton atpase 116 kda subunit a isoform 1 (96 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit g (13 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit h (55 kDa, Protein from Rattus norvegicus)
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)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d4t
Q-score: 0.545
Di Trani JM, Moe A, Riepl D, Saura P, Kaila VRI, Brzezinski P, Rubinstein JL
PNAS (2022) 119 pp. e2205228119-e2205228119 [ Pubmed: 35858451 DOI: doi:10.1073/pnas.2205228119 ]
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- Cytochrome c oxidase subunit 2 (26 kDa, Protein from Bos taurus)
- Cytochrome c oxidase subunit 6b1 (9 kDa, Protein from Bos taurus)
- Cytochrome c oxidase subunit 7b, mitochondrial (5 kDa, Protein from Bos taurus)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase subunit 5b, mitochondrial (10 kDa, Protein from Bos taurus)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Cytochrome c oxidase subunit 6c (8 kDa, Protein from Bos taurus)
- Cytochrome c oxidase subunit 1 (56 kDa, Protein from Bos taurus)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 7a1, mitochondrial (6 kDa, Protein from Bos taurus)
- Cytochrome c oxidase subunit 7c, mitochondrial (5 kDa, Protein from Bos taurus)
- Cytochrome c oxidase subunit 6a2, mitochondrial (8 kDa, Protein from Bos taurus)
- Zinc ion (65 Da, Ligand)
- Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (16 kDa, Protein from Bos taurus)
- Cytochrome c oxidase subunit 5a, mitochondrial (11 kDa, Protein from Bos taurus)
- Cytochrome c oxidase subunit 3 (29 kDa, Protein from Bos taurus)
- Sodium ion (22 Da, Ligand)
- Cytochrome c oxidase (Complex from Bos taurus)
- (1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5e,8e,11e,14e)-icosa-5,8,11,14-tetraenoate (768 Da, Ligand)
- Cytochrome c oxidase subunit 8a, mitochondrial (4 kDa, Protein from Bos taurus)
Complex III2 from Candida albicans, inhibitor free
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7rja
Q-score: 0.523
Di Trani JM, Liu Z, Whitesell L, Brzezinski P, Cowen LE, Rubinstein JL
Structure (2022) 30 pp. 129- [ DOI: doi:10.1016/j.str.2021.08.006 Pubmed: 34525326 ]
- Respiratory complex iii2 from candida albicans (Complex from Candida albicans SC5314)
- Heme c (618 Da, Ligand)
- Ubiquinol--cytochrome-c reductase catalytic subunit (32 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Cytochrome b (43 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit (48 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit 9 (7 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Cytochrome b-c1 complex subunit 2, mitochondrial (39 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinone-10 (863 Da, Ligand)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (23 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit 8 (11 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit 6 (16 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
Complex III2 from Candida albicans, inhibitor free, Rieske head domain in b position
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7rjb
Q-score: 0.48
Di Trani JM, Liu Z, Whitesell L, Brzezinski P, Cowen LE, Rubinstein JL
Structure (2022) 30 pp. 129- [ DOI: doi:10.1016/j.str.2021.08.006 Pubmed: 34525326 ]
- Respiratory complex iii2 from candida albicans (Complex from Candida albicans SC5314)
- Heme c (618 Da, Ligand)
- Ubiquinol--cytochrome-c reductase catalytic subunit (32 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Cytochrome b (43 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit (48 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit 9 (7 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Cytochrome b-c1 complex subunit 2, mitochondrial (39 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinone-10 (863 Da, Ligand)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (23 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit 8 (11 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))
- Ubiquinol--cytochrome-c reductase subunit 6 (16 kDa, Protein from Candida albicans (strain SC5314 / ATCC MYA-2876))