Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8a1u
Q-score: 0.558
Hau JL, Kaltwasser S, Muras V, Casutt MS, Vohl G, Claussen B, Steffen W, Leitner A, Bill E, Cutsail 3rd GE, DeBeer S, Vonck J, Steuber J, Fritz G
Nat Struct Mol Biol (2023) 30 pp. 1686-1694 [ DOI: doi:10.1038/s41594-023-01099-0 Pubmed: 37710014 ]
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae)
- Ubiquinone-2 (318 Da, Ligand)
- 1,4-dihydronicotinamide adenine dinucleotide (665 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae)
- Water (18 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit a (51 kDa, Protein from Vibrio cholerae)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae)
- Sodium ion (22 Da, Ligand)
- Nqr complex with substrates nadh and q2 (220 kDa, Complex from Vibrio cholerae)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
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 [ DOI: doi:10.1073/pnas.2214949120 Pubmed: 36952383 ]
- Menaquinone-9 (785 Da, Ligand)
- 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)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (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)
- Zinc ion (65 Da, Ligand)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit e (25 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 h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Iron/sulfur cluster (351 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 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 [ DOI: doi:10.1073/pnas.2214949120 Pubmed: 36952383 ]
- Menaquinone-9 (785 Da, Ligand)
- 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)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterial respiratory complex i, fully-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (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)
- Zinc ion (65 Da, Ligand)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Iron/sulfur cluster (351 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 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 [ DOI: doi:10.1073/pnas.2214949120 Pubmed: 36952383 ]
- Menaquinone-9 (785 Da, Ligand)
- 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)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (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)
- Zinc ion (65 Da, Ligand)
- Nadh-quinone oxidoreductase, l subunit (65 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 subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Iron/sulfur cluster (351 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Structure of porcine V-ATPase with mEAK7 and SidK, Rotary state 2
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7u8o
Q-score: 0.371
Tan YZ, Abbas YM, Wu JZ, Wu D, Keon KA, Hesketh GG, Bueler SA, Gingras AC, Robinson CV, Grinstein S, Rubinstein JL
Life Sci Alliance (2022) 5 [ DOI: doi:10.26508/lsa.202201527 Pubmed: 35794005 ]
- Bacterial effector protein sidk (38 kDa, Protein from Legionella pneumophila)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit d (28 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit a (96 kDa, Protein from Sus scrofa)
- V-type proton atpase 21 kda proteolipid subunit isoform 1 (21 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Sus scrofa)
- Atpase h(+)-transporting lysosomal accessory protein 2 (39 kDa, Protein from Sus scrofa)
- Ribonuclease kappa (11 kDa, Protein from Sus scrofa)
- Vacuolar proton pump subunit b (57 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (40 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit g (13 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit c (44 kDa, Protein from Sus scrofa)
- V-type proton atpase proteolipid subunit (15 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit f (13 kDa, Protein from Sus scrofa)
- V-atpase in complex with recombinant sidk and recombinant meak-7 (Complex from Sus scrofa)
- Tldc protein meak-7 (50 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit h (55 kDa, Protein from Sus scrofa)
- Atpase h+ transporting accessory protein 1 (51 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (9 kDa, Protein from Sus scrofa)
Structure of porcine kidney V-ATPase with SidK, Rotary State 1
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7u8p
Q-score: 0.334
Tan YZ, Abbas YM, Wu JZ, Wu D, Keon KA, Hesketh GG, Bueler SA, Gingras AC, Robinson CV, Grinstein S, Rubinstein JL
Life Sci Alliance (2022) 5 [ DOI: doi:10.26508/lsa.202201527 Pubmed: 35794005 ]
- Bacterial effector protein sidk (38 kDa, Protein from Legionella pneumophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit d (28 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit a (96 kDa, Protein from Sus scrofa)
- V-type proton atpase 21 kda proteolipid subunit isoform 1 (21 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Sus scrofa)
- Atpase h(+)-transporting lysosomal accessory protein 2 (39 kDa, Protein from Sus scrofa)
- Ribonuclease kappa (11 kDa, Protein from Sus scrofa)
- Vacuolar proton pump subunit b (57 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (40 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit g (13 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit c (44 kDa, Protein from Sus scrofa)
- V-type proton atpase proteolipid subunit (15 kDa, Protein from Sus scrofa)
- Porcine kidney v-atpase with sidk, rotary state 1 (Complex from Sus scrofa)
- V-type proton atpase subunit f (13 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit h (55 kDa, Protein from Sus scrofa)
- Atpase h+ transporting accessory protein 1 (51 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (9 kDa, Protein from Sus scrofa)
Structure of porcine kidney V-ATPase with SidK, Rotary State 2
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7u8q
Q-score: 0.247
Tan YZ, Abbas YM, Wu JZ, Wu D, Keon KA, Hesketh GG, Bueler SA, Gingras AC, Robinson CV, Grinstein S, Rubinstein JL
Life Sci Alliance (2022) 5 [ DOI: doi:10.26508/lsa.202201527 Pubmed: 35794005 ]
- Bacterial effector protein sidk (38 kDa, Protein from Legionella pneumophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Porcine kidney v-atpase with sidk, rotary state 2 (Complex from Sus scrofa)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit d (28 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit a (96 kDa, Protein from Sus scrofa)
- V-type proton atpase 21 kda proteolipid subunit isoform 1 (21 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Sus scrofa)
- Atpase h(+)-transporting lysosomal accessory protein 2 (39 kDa, Protein from Sus scrofa)
- Ribonuclease kappa (11 kDa, Protein from Sus scrofa)
- Vacuolar proton pump subunit b (57 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (40 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit g (13 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit c (44 kDa, Protein from Sus scrofa)
- V-type proton atpase proteolipid subunit (15 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit f (13 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit h (55 kDa, Protein from Sus scrofa)
- Atpase h+ transporting accessory protein 1 (51 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (9 kDa, Protein from Sus scrofa)
Structure of porcine kidney V-ATPase with SidK, Rotary State 3
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7u8r
Q-score: 0.301
Tan YZ, Abbas YM, Wu JZ, Wu D, Keon KA, Hesketh GG, Bueler SA, Gingras AC, Robinson CV, Grinstein S, Rubinstein JL
Life Sci Alliance (2022) 5 [ DOI: doi:10.26508/lsa.202201527 Pubmed: 35794005 ]
- Bacterial effector protein sidk (38 kDa, Protein from Legionella pneumophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit d (28 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit a (96 kDa, Protein from Sus scrofa)
- V-type proton atpase 21 kda proteolipid subunit isoform 1 (21 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Sus scrofa)
- Atpase h(+)-transporting lysosomal accessory protein 2 (39 kDa, Protein from Sus scrofa)
- Ribonuclease kappa (11 kDa, Protein from Sus scrofa)
- Vacuolar proton pump subunit b (57 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (40 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit g (13 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit c (44 kDa, Protein from Sus scrofa)
- V-type proton atpase proteolipid subunit (15 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit f (13 kDa, Protein from Sus scrofa)
- Porcine kidney v-atpase with sidk, rotary state 3 (Complex from Sus scrofa)
- V-type proton atpase subunit h (55 kDa, Protein from Sus scrofa)
- Atpase h+ transporting accessory protein 1 (51 kDa, Protein from Sus scrofa)
- V-type proton atpase subunit (9 kDa, Protein from Sus scrofa)
Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7tao
Q-score: 0.491
Keon KA, Benlekbir S, Kirsch SH, Muller R, Rubinstein JL
ACS Chem Biol (2022) 17 pp. 619-628 [ DOI: doi:10.1021/acschembio.1c00894 Pubmed: 35148071 ]
- Yeast v-atpase subunit f (9 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of bafilomycin a1 bound to yeast vo v-atpase (Complex from Saccharomyces cerevisiae)
- (5r)-2,4-dideoxy-1-c-{(2s,3r,4s)-3-hydroxy-4-[(2r,3s,4e,6e,9r,10s,11r,12e,14z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-d-threo-pentopyranose (622 Da, Ligand)
- V-type proton atpase subunit a, vacuolar isoform (95 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of archazolid A bound to yeast VO V-ATPase
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7tap
Q-score: 0.587
Keon KA, Benlekbir S, Kirsch SH, Muller R, Rubinstein JL
ACS Chem Biol (2022) 17 pp. 619-628 [ DOI: doi:10.1021/acschembio.1c00894 Pubmed: 35148071 ]
- Yeast v-atpase subunit f (9 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae)
- Archazolid a (739 Da, Ligand)
- V-type proton atpase subunit a, vacuolar isoform (95 kDa, Protein from Saccharomyces cerevisiae)
- Cryo-em structure of archazolid a bound to yeast vo v-atpase (Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae)