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 [ Pubmed: 38900912 DOI: doi:10.1126/science.adp5577 ]
- Sidk (65 kDa, Protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Rattus norvegicus)
- Atpase h+-transporting v1 subunit d (28 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit g (13 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit f (13 kDa, Protein from Rattus norvegicus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, v1 (Complex from Rattus norvegicus)
- H(+)-transporting two-sector atpase (71 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 [ Pubmed: 38900912 DOI: doi:10.1126/science.adp5577 ]
- V-type proton atpase subunit s1 (51 kDa, Protein from Rattus norvegicus)
- (7r)-4,7-dihydroxy-n,n,n-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacosan-1-aminium 4-oxide (524 Da, Ligand)
- Synaptophysin (33 kDa, Protein from Rattus norvegicus)
- V-type proton atpase 116 kda subunit a 1 (94 kDa, Protein from Rattus norvegicus)
- Renin receptor (39 kDa, Protein from Rattus norvegicus)
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, vo (Complex 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)
- Atpase h+-transporting v1 subunit d (28 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Rattus norvegicus)
- Rnasek protein (9 kDa, Protein from Rattus norvegicus)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- V-type proton atpase subunit (40 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit f (13 kDa, Protein from Rattus norvegicus)
- Atpase, h+ transporting, v0 subunit b (predicted), isoform cra_a (21 kDa, Protein from Rattus norvegicus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Rattus norvegicus)
- Phosphatidylethanolamine (734 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 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 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)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterial respiratory complex i, consensus map (560 kDa, Complex 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)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Nadh-quinone oxidoreductase subunit d (48 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 ]
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 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)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Two-component system response regulator (14 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)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Mycobacterial respiratory complex i, fully-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 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 d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Flavin mononucleotide (456 Da, Ligand)
- Menaquinone-9 (785 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)
- Mycobacterial respiratory complex i, semi-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)