Electron bifurcating hydrogenase - HydABC from A. woodii
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 7q4v
Q-score: 0.211
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ Pubmed: 36811855 DOI: doi:10.1021/jacs.2c11683 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Homodimer complex of hydabc trimer (300 MDa, Complex from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hydb (64 kDa, Protein from Acetobacterium woodii DSM 1030)
- Flavin mononucleotide (456 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8a5e
Q-score: 0.409
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ Pubmed: 36811855 DOI: doi:10.1021/jacs.2c11683 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Zinc ion (65 Da, Ligand)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hydb (64 kDa, Protein from Acetobacterium woodii DSM 1030)
- Flavin mononucleotide (456 Da, Ligand)
- Electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui (348 kDa, Complex from Thermoanaerobacter kivui)
- 1,4-dihydronicotinamide adenine dinucleotide (665 Da, Ligand)
- 2 iron/2 sulfur/5 carbonyl/2 water inorganic cluster (355 Da, Ligand)
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 7q4w
Q-score: 0.253
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ DOI: doi:10.1021/jacs.2c11683 Pubmed: 36811855 ]
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Homodimer complex of hydabc trimer (350 MDa, Complex from Acetobacterium woodii DSM 1030)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Iron hydrogenase hydb (50 kDa, Protein from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Zinc ion (65 Da, Ligand)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a6t
Q-score: 0.46
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ Pubmed: 36811855 DOI: doi:10.1021/jacs.2c11683 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Electron bifurcating hydrogenase subunit hydb (68 kDa, Protein from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hydc (18 kDa, Protein from Thermoanaerobacter kivui)
- Zinc ion (65 Da, Ligand)
- Nadp nicotinamide-adenine-dinucleotide phosphate (743 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui (348 kDa, Complex from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hyda1 (63 kDa, Protein from Thermoanaerobacter kivui)
- 2 iron/2 sulfur/5 carbonyl/2 water inorganic cluster (355 Da, Ligand)
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 8bew
Q-score: 0.411
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ DOI: doi:10.1021/jacs.2c11683 Pubmed: 36811855 ]
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Electron bifurcating hydrogenase subunit hydb (68 kDa, Protein from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hyda1 (63 kDa, Protein from Thermoanaerobacter kivui)
- Zinc ion (65 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Dimer of the trimeric hydabc complex (Complex from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hydc (18 kDa, Protein from Thermoanaerobacter kivui)
Cryo-EM structure of respiratory complex I in the active state from Mus musculus at 3.1 A
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6zr2, 6ztq
Q-score: 0.2455
Bridges HR, Fedor JG, Blaza JN, Di Luca A, Jussupow A, Jarman OD, Wright JJ, Agip AA, Gamiz-Hernandez AP, Roessler MM, Kaila VRI, Hirst J
Nat Commun (2020) 11 pp. 5261-5261 [ Pubmed: 33067417 DOI: doi:10.1038/s41467-020-18950-3 ]
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (13 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (9 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (12 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial (21 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (42 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 subunit c1, mitochondrial (8 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (24 kDa, Protein from Mouse)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphoethanolamine (748 Da, Ligand)
- ~{s}-[2-[3-[[(2~{r})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{s})-3-oxidanyltetradecanethioate (584 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (16 kDa, Protein from Mouse)
- Acyl carrier protein, mitochondrial (17 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 subunit c2 (14 kDa, Protein from Mouse)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (21 kDa, Protein from Mouse)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (50 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 5 (68 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (30 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 3 (13 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial (40 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (52 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 4 (51 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (20 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (15 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial (17 kDa, Protein from Mouse)
- Respiratory complex i (980 kDa, Complex from Mus musculus)
- Nadh dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (27 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (15 kDa, Protein from Mouse)
- Mcg5603 (15 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (8 kDa, Protein from Mouse)
- Zinc ion (65 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (11 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 6 (18 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (10 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 2 (38 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 (6 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (11 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (17 kDa, Protein from Mouse)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Nadh-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (79 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (15 kDa, Protein from Mouse)
- Cardiolipin (1 kDa, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (16 kDa, Protein from Mouse)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (19 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial (13 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (21 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 4l (10 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial (11 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 1 (36 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 5 (12 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (22 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (24 kDa, Protein from Mouse)
Cryo-EM structure of respiratory complex I from Mus musculus inhibited by piericidin A at 3.0 A
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6ztq, 6zr2
Q-score: 0.257
Bridges HR, Fedor JG, Blaza JN, Di Luca A, Jussupow A, Jarman OD, Wright JJ, Agip AA, Gamiz-Hernandez AP, Roessler MM, Kaila VRI, Hirst J
Nat Commun (2020) 11 pp. 5261-5261 [ Pubmed: 33067417 DOI: doi:10.1038/s41467-020-18950-3 ]
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (52 kDa, Protein from Mouse)
- Cardiolipin (1 kDa, Ligand)
- Nadh-ubiquinone oxidoreductase chain 4l (10 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (19 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (79 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 (6 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial (17 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 3 (13 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (16 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (15 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (22 kDa, Protein from Mouse)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (24 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 2 (38 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (17 kDa, Protein from Mouse)
- Piericidin a (415 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial (21 kDa, Protein from Mouse)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Acyl carrier protein, mitochondrial (17 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (11 kDa, Protein from Mouse)
- 1,2-diacyl-sn-glycero-3-phosphoethanolamine (748 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (10 kDa, Protein from Mouse)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-ubiquinone oxidoreductase chain 4 (51 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (21 kDa, Protein from Mouse)
- Zinc ion (65 Da, Ligand)
- Nadh-ubiquinone oxidoreductase chain 6 (18 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (16 kDa, Protein from Mouse)
- Respiratory complex i (980 kDa, Complex from Mus musculus)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial (40 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (24 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (27 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (15 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (11 kDa, Protein from Mouse)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (15 kDa, Protein from Mouse)
- ~{s}-[2-[3-[[(2~{r})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{s})-3-oxidanyltetradecanethioate (584 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (42 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (9 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (8 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 5 (12 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial (13 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (13 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (12 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 1 (36 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (20 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 subunit c1, mitochondrial (8 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (50 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 subunit c2 (14 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial (11 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (21 kDa, Protein from Mouse)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (30 kDa, Protein from Mouse)
- Nadh-ubiquinone oxidoreductase chain 5 (68 kDa, Protein from Mouse)
- Mcg5603 (15 kDa, Protein from Mouse)
Structure of the NDH-1MS complex from Thermosynechococcus elongatus
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6tjv
Q-score: 0.529
Schuller JM, Saura P, Thiemann J, Schuller SK, Gamiz-Hernandez AP, Kurisu G, Nowaczyk MM, Kaila VRI
Nat Commun (2020) 11 pp. 494-494 [ Pubmed: 31980611 DOI: doi:10.1038/s41467-020-14347-4 ]
- Nad(p)h-quinone oxidoreductase subunit h (45 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit i (22 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 4l (11 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nadh dehydrogenase subunit 4 (53 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Chlorophyll a (893 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit l (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Beta-carotene (536 Da, Ligand)
- Ndh-1ms (Complex from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit k (25 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Zinc ion (65 Da, Ligand)
- Nadh dehydrogenase subunit 6 (21 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Tlr0906 protein (51 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 3 (15 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Water (18 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit 1 (40 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Tlr0636 protein (12 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit j (19 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nadh dehydrogenase subunit 5 (66 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit m (12 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit n (16 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 2 (55 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit o (7 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Iron/sulfur cluster (351 Da, Ligand)
- Tll0220 protein (15 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))