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)
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)
Mycobacterial respiratory complex I with both quinone positions modelled
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8e9g
Q-score: 0.537
Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL
PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterial respiratory complex i, consensus map (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- (2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterial respiratory complex I, fully-inserted quinone
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8e9h
Q-score: 0.533
Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL
PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- (2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Mycobacterial respiratory complex i, fully-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterial respiratory complex I, semi-inserted quinone
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8e9i
Q-score: 0.509
Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL
PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- (2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterial respiratory complex i, semi-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
CryoEM structure of the C. sordellii lethal toxin TcsL in complex with SEMA6A
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6wts
Q-score: 0.463
Lee H, Beilhartz GL, Kucharska I, Raman S, Cui H, Lam MHY, Liang H, Rubinstein JL, Schramek D, Julien JP, Melnyk RA, Taipale M
Cell (2020) 182 pp. 345- [ Pubmed: 32589945 DOI: doi:10.1016/j.cell.2020.06.005 ]
- Complex of sema6a with tcsl (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Tcsl (Complex from Paeniclostridium sordellii)
- Sema6a (63 kDa, Protein from Homo sapiens)
- Sema6a (Complex from Homo sapiens)
- Tcsl (63 kDa, Protein from Paeniclostridium sordellii)
CryoEM structure of human SEMA6A dimer
Lee H, Beilhartz GL, Kucharska I, Raman S, Cui H, Lam MHY, Liang H, Rubinstein JL, Schramek D, Julien JP, Melnyk RA, Taipale M
Cell (2020) [ Pubmed: 32589945 DOI: doi:10.1016/j.cell.2020.06.005 ]
- Sema6a dimer (Cell from Homo sapiens)
- Sema6a (Protein from Homo sapiens)