Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris
Qi CH, Wang GL, Wang FF, Wang J, Wang XP, Zou MJ, Ma F, Madigan MT, Kimura Y, Wang-Otomo ZY, Yu LJ
J Integr Plant Biol (2024) [ Pubmed: 38411333 DOI: doi:10.1111/jipb.13628 ]
- Unknown ligand (909 Da, Ligand)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Antenna complex alpha/beta subunit domain-containing protein (7 kDa, Protein from Halorhodospira halochloris)
- Reaction center protein m chain (36 kDa, Protein from Halorhodospira halochloris)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Reactin center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
- Reaction center protein l chain (31 kDa, Protein from Halorhodospira halochloris)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Beta subunit of light-harvesting 1 (9 kDa, Protein from Halorhodospira halochloris)
- Gamma subunit of light-harvesting 1 (3 kDa, Protein from Halorhodospira halochloris)
- Heme c (618 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Trans-geranyl bacteriopheophytin b (885 Da, Ligand)
- Antenna complex alpha/beta subunit domain-containing protein (12 kDa, Protein from Halorhodospira halochloris)
- Rc-lh core complex (Complex from Halorhodospira halochloris)
- Lycopene (536 Da, Ligand)
- Light-harvesting lhi (7 kDa, Protein from Halorhodospira halochloris)
- Fe (iii) ion (55 Da, Ligand)
- Trans-geranyl 8-vinyl-bacteriochlorophyll b (907 Da, Ligand)
- Reaction center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
- Trans-geranyl bacteriochlorophyll b (907 Da, Ligand)
- Photosynthetic reaction center h subunit (31 kDa, Protein from Halorhodospira halochloris)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Halorhodospira halochloris)
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8wdu
Q-score: 0.676
Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY
Commun Biol (2024) 7 pp. 176-176 [ DOI: doi:10.1038/s42003-024-05863-w Pubmed: 38347078 ]
- (2s)-3-hydroxypropane-1,2-diyl dihexadecanoate (568 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Bacteriopheophytin a (889 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Reaction center protein l chain (31 kDa, Protein from Allochromatium vinosum DSM 180)
- Reaction center protein m chain (36 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Palmitic acid (256 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Allochromatium vinosum DSM 180)
- Calcium ion (40 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Water (18 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple sulfur phototrophic bacterium allochromatium vinosum (Complex from Allochromatium vinosum DSM 180)
- Magnesium ion (24 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8wdv
Q-score: 0.658
Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY
Commun Biol (2024) 7 pp. 176-176 [ Pubmed: 38347078 DOI: doi:10.1038/s42003-024-05863-w ]
- Cardiolipin (1 kDa, Ligand)
- Palmitic acid (256 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Allochromatium vinosum DSM 180)
- Spirilloxanthin (596 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Allochromatium vinosum DSM 180)
- Ubiquinone-8 (727 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic lh1-rc complex from the purple sulfur phototrophic bacterium allochromatium vinosum (Complex from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Fe (iii) ion (55 Da, Ligand)
- (2s)-3-hydroxypropane-1,2-diyl dihexadecanoate (568 Da, Ligand)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium vinosum DSM 180)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Allochromatium vinosum DSM 180)
- Water (18 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Calcium ion (40 Da, Ligand)
Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 8go3
Q-score: 0.553
To Be Published
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli K-12)
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli K-12)
- Purified escherichia coli cytochrome bo3 (Complex from Escherichia coli K-12)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli K-12)
- Heme o (838 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Ubiquinol oxidase (22 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of the I-II-III2-IV2 respiratory supercomplex from Tetrahymena thermophila
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8bqs
Q-score: 0.356
Muhleip A, Kock Flygaard R, Baradaran R, Haapanen O, Gruhl T, Tobiasson V, Marechal A, Sharma V, Amunts A
To Be Published
- M16 family peptidase, putative (53 kDa, Protein from Tetrahymena thermophila SB210)
- Acyl carrier protein (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (9 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (41 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (8 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf75 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Structural protein (27 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 7 (51 kDa, Protein from Tetrahymena thermophila SB210)
- Cx9c domain-containing protein (28 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (7 kDa, Protein from Tetrahymena thermophila SB210)
- Sdhtt11 (5 kDa, Protein from Tetrahymena thermophila SB210)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Ndub10 (22 kDa, Protein from Tetrahymena thermophila SB210)
- Cox assembly mitochondrial protein (17 kDa, Protein from Tetrahymena thermophila SB210)
- Phage protein (14 kDa, Protein from Tetrahymena thermophila SB210)
- Gamma-carbonic anhydrase (28 kDa, Protein from Tetrahymena thermophila SB210)
- Ndutt12 (13 kDa, Protein from Tetrahymena thermophila SB210)
- Zf-tim10_ddp domain-containing protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf62 (30 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (7 kDa, Protein from Tetrahymena thermophila SB210)
- Chch domain-containing protein (13 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (52 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (23 kDa, Protein from Tetrahymena thermophila SB210)
- Atp synthase subunit e, mitochondrial (11 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 10 (18 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein (7 kDa, Protein from Tetrahymena thermophila SB210)
- Uqcrtt2 (4 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase 24 kda subunit (31 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit vb protein (75 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase complex i, 21 kda subunit (17 kDa, Protein from Tetrahymena thermophila SB210)
- Transposase (8 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase chain 3 (14 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (24 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (8 kDa, Protein from Tetrahymena thermophila SB210)
- Uqcrtt1 (39 kDa, Protein from Tetrahymena thermophila SB210)
- Heme-a (852 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nadh dehydrogenase subunit 1 (7 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt27 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (26 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (21 kDa, Protein from Tetrahymena thermophila SB210)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Ymf70 (10 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (20 kDa, Protein from Tetrahymena thermophila SB210)
- Duf4885 domain-containing protein (12 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase 75 kda subunit (80 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub4 (14 kDa, Protein from Tetrahymena thermophila SB210)
- Annexin (8 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila SB210)
- Cardiolipin (1 kDa, Ligand)
- Transmembrane protein, putative (9 kDa, Protein from Tetrahymena thermophila SB210)
- Rieske iron-sulfur protein, ubiquinol-cytochrome c reductase iron-sulfur subunit (30 kDa, Protein from Tetrahymena thermophila SB210)
- Complex iii subunit vii (19 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila SB210)
- Apocytochrome b (50 kDa, Protein from Tetrahymena thermophila SB210)
- Iron-binding zinc finger cdgsh type protein (21 kDa, Protein from Tetrahymena thermophila SB210)
- Respiratory chain supercomplex from the ciliate tetrahymena thermophila (Complex from Tetrahymena thermophila SB210)
- 2 iron, 2 sulfur cluster-binding protein (19 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (16 kDa, Protein from Tetrahymena thermophila SB210)
- Calcium ion (40 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila SB210)
- Succinate dehydrogenase (36 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (16 kDa, Protein from Tetrahymena thermophila SB210)
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (70 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (18 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt22 (17 kDa, Protein from Tetrahymena thermophila SB210)
- Abc transporter (10 kDa, Protein from Tetrahymena thermophila SB210)
- Heme c (618 Da, Ligand)
- Transmembrane protein, putative (24 kDa, Protein from Tetrahymena thermophila SB210)
- Gamma-carbonic anhydrase (25 kDa, Protein from Tetrahymena thermophila SB210)
- Lipid-a-disaccharide synthase (59 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub8 (24 kDa, Protein from Tetrahymena thermophila SB210)
- Yflt domain-containing protein (19 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial (37 kDa, Protein from Tetrahymena thermophila SB210)
- Acyl carrier protein (16 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf67 (54 kDa, Protein from Tetrahymena thermophila SB210)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Transmembrane protein, putative (18 kDa, Protein from Tetrahymena thermophila SB210)
- Flavin mononucleotide (456 Da, Ligand)
- Ph domain-containing protein (15 kDa, Protein from Tetrahymena thermophila SB210)
- Ubiquinol-cytochrome c reductase hinge protein (9 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (13 kDa, Protein from Tetrahymena thermophila SB210)
- Diphthamide synthesis protein (22 kDa, Protein from Tetrahymena thermophila SB210)
- Protein phosphatase 2c, putative (53 kDa, Protein from Tetrahymena thermophila SB210)
- Surf1-like protein (35 kDa, Protein from Tetrahymena thermophila SB210)
- Uncharacterized protein (23 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 9 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Rnase iii domain-containing protein (35 kDa, Protein from Tetrahymena thermophila SB210)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Complex i-mnll (12 kDa, Protein from Tetrahymena thermophila SB210)
- Lysozyme (12 kDa, Protein from Tetrahymena thermophila SB210)
- Fe3-s4 cluster (295 Da, Ligand)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial (22 kDa, Protein from Tetrahymena thermophila SB210)
- Ndutt11 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Tim10/ddp family zinc finger protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (29 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt10 (28 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (14 kDa, Protein from Tetrahymena thermophila SB210)
- Ndutt10 (14 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf58 (13 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (22 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (57 kDa, Protein from Tetrahymena thermophila SB210)
- Mobilization protein (23 kDa, Protein from Tetrahymena thermophila SB210)
- Nduph2 (22 kDa, Protein from Tetrahymena thermophila SB210)
- Ubiquinone-8 (727 Da, Ligand)
- Transmembrane protein, putative (12 kDa, Protein from Tetrahymena thermophila SB210)
- Gram domain protein (10 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf65 (43 kDa, Protein from Tetrahymena thermophila SB210)
- Decapping nuclease (10 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt9 (29 kDa, Protein from Tetrahymena thermophila SB210)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Transmembrane protein (24 kDa, Protein from Tetrahymena thermophila SB210)
- Magnesium ion (24 Da, Ligand)
- Ymf57 (12 kDa, Protein from Tetrahymena thermophila SB210)
- Cullin domain-containing protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase, putative (20 kDa, Protein from Tetrahymena thermophila SB210)
- Nd5a (25 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase chain 4 (58 kDa, Protein from Tetrahymena thermophila SB210)
- Oxoglutarate/malate translocator protein, putative (40 kDa, Protein from Tetrahymena thermophila SB210)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Transposase (11 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit 2 (72 kDa, Protein from Tetrahymena thermophila SB210)
- Copper (ii) ion (63 Da, Ligand)
- Dnaj domain protein (36 kDa, Protein from Tetrahymena thermophila SB210)
- Chromosome condensation regulator rcc1 repeat protein,chromosome condensation regulator rcc1 repeat protein,chromosome condensation regulator rcc1 repeat protein,chain 150 (50 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (26 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (14 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 2 (20 kDa, Protein from Tetrahymena thermophila SB210)
- Nad-dependent epimerase/dehydratase family protein (41 kDa, Protein from Tetrahymena thermophila SB210)
- Acyl-coa synthetase (amp-forming)/amp-acid ligase ii (36 kDa, Protein from Tetrahymena thermophila SB210)
- Ndua13 (21 kDa, Protein from Tetrahymena thermophila SB210)
- Zinc-finger protein (15 kDa, Protein from Tetrahymena thermophila SB210)
- Nmra domain-containing protein (36 kDa, Protein from Tetrahymena thermophila SB210)
- Peptidase m16 inactive domain protein (58 kDa, Protein from Tetrahymena thermophila SB210)
- 39s ribosomal protein l9, mitochondrial (27 kDa, Protein from Tetrahymena thermophila SB210)
- Succinate dehydrogenase complex iron-sulfur subunit d (5 kDa, Protein from Tetrahymena thermophila SB210)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transmembrane protein (28 kDa, Protein from Tetrahymena thermophila SB210)
- Zf-tim10_ddp domain-containing protein (10 kDa, Protein from Tetrahymena thermophila SB210)
- Transcription factor apfi protein, putative (39 kDa, Protein from Tetrahymena thermophila SB210)
- Ribosomal protein l51/s25/ci-b8 domain protein (12 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Uqcrtt3 (5 kDa, Protein from Tetrahymena thermophila SB210)
- Trab family protein (45 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt28 (11 kDa, Protein from Tetrahymena thermophila SB210)
- 37s ribosomal protein s25, mitochondrial (33 kDa, Protein from Tetrahymena thermophila SB210)
- 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate (648 Da, Ligand)
- Ymf68 (72 kDa, Protein from Tetrahymena thermophila SB210)
- Zinc ion (65 Da, Ligand)
- Etc complex i subunit motif protein (24 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit 1 (80 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt12,transmembrane protein,transmembrane protein (25 kDa, Protein from Tetrahymena thermophila SB210)
- Ndub6 (15 kDa, Protein from Tetrahymena thermophila SB210)
- Dinuclear copper ion (127 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Nadh-ubiquinone oxidoreductase chain 1 (32 kDa, Protein from Tetrahymena thermophila SB210)
- 2-oxoglutarate/malate carrier protein (36 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome protein c1 (37 kDa, Protein from Tetrahymena thermophila SB210)
- Thioredoxin (19 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (35 kDa, Protein from Tetrahymena thermophila SB210)
- Carrier protein (37 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase subunit 5 (88 kDa, Protein from Tetrahymena thermophila SB210)
- Ctf/nf-i domain-containing protein (116 kDa, Protein from Tetrahymena thermophila SB210)
- Surf1-like protein (47 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh-ubiquinone oxidoreductase 1, chain, putative (28 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein (20 kDa, Protein from Tetrahymena thermophila SB210)
- Uridine-5'-diphosphate (404 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b6g
Q-score: 0.402
Muhleip A, Flygaard RK, Baradaran R, Haapanen O, Gruhl T, Tobiasson V, Marechal A, Sharma V, Amunts A
Nature (2023) 615 pp. 934-938 [ Pubmed: 36949187 DOI: doi:10.1038/s41586-023-05817-y ]
- Cardiolipin (1 kDa, Ligand)
- Succinate dehydrogenase (quinone) (36 kDa, Protein from Tetrahymena thermophila)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila)
- Transmembrane protein, putative (7 kDa, Protein from Tetrahymena thermophila)
- Nmra domain-containing protein (36 kDa, Protein from Tetrahymena thermophila)
- Transmembrane protein, putative (35 kDa, Protein from Tetrahymena thermophila)
- Fe3-s4 cluster (295 Da, Ligand)
- Succinate dehydrogenase complex (complex-ii) (305 kDa, Complex from Tetrahymena thermophila)
- Calcium ion (40 Da, Ligand)
- Transmembrane protein, putative (9 kDa, Protein from Tetrahymena thermophila)
- Cytochrome b-c1 complex subunit 8 (7 kDa, Protein from Tetrahymena thermophila)
- Duf4885 domain-containing protein (12 kDa, Protein from Tetrahymena thermophila)
- Heme c (618 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Sdhtt11 (5 kDa, Protein from Tetrahymena thermophila)
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (70 kDa, Protein from Tetrahymena thermophila)
- Sdhtt3 (23 kDa, Protein from Tetrahymena thermophila)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Transposase (11 kDa, Protein from Tetrahymena thermophila)
- Diphthamide synthesis protein (22 kDa, Protein from Tetrahymena thermophila)
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Transmembrane protein, putative (11 kDa, Protein from Tetrahymena thermophila)
- Sdhd (5 kDa, Protein from Tetrahymena thermophila)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8b6h
Q-score: 0.531
Muhleip A, Flygaard RK, Baradaran R, Haapanen O, Gruhl T, Tobiasson V, Marechal A, Sharma V, Amunts A
Nature (2023) 615 pp. 934-938 [ Pubmed: 36949187 DOI: doi:10.1038/s41586-023-05817-y ]
- Nadh dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (28 kDa, Protein from Tetrahymena thermophila SB210)
- Protein phosphatase 2c, putative (53 kDa, Protein from Tetrahymena thermophila SB210)
- Annexin (8 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (41 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf75 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Surf1-like protein (35 kDa, Protein from Tetrahymena thermophila SB210)
- Structural protein (27 kDa, Protein from Tetrahymena thermophila SB210)
- 39s ribosomal protein l9, mitochondrial (27 kDa, Protein from Tetrahymena thermophila SB210)
- Cardiolipin (1 kDa, Ligand)
- Complex iii subunit vii (19 kDa, Protein from Tetrahymena thermophila SB210)
- Iron-binding zinc finger cdgsh type protein (21 kDa, Protein from Tetrahymena thermophila SB210)
- Phage protein (14 kDa, Protein from Tetrahymena thermophila SB210)
- Lysozyme (12 kDa, Protein from Tetrahymena thermophila SB210)
- Zf-tim10_ddp domain-containing protein (10 kDa, Protein from Tetrahymena thermophila SB210)
- Zf-tim10_ddp domain-containing protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Tim10/ddp family zinc finger protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Trab family protein (45 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt10 (28 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (14 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt28 (11 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit vb protein (75 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (16 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (57 kDa, Protein from Tetrahymena thermophila SB210)
- Mobilization protein (23 kDa, Protein from Tetrahymena thermophila SB210)
- 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate (648 Da, Ligand)
- Ymf68 (72 kDa, Protein from Tetrahymena thermophila SB210)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Coxtt12,transmembrane protein,transmembrane protein (25 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit 1 (80 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (18 kDa, Protein from Tetrahymena thermophila SB210)
- Abc transporter (10 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt22 (17 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (12 kDa, Protein from Tetrahymena thermophila SB210)
- Transposase (8 kDa, Protein from Tetrahymena thermophila SB210)
- Dinuclear copper ion (127 Da, Ligand)
- Transmembrane protein, putative (24 kDa, Protein from Tetrahymena thermophila SB210)
- Ubiquinone-8 (727 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 2-oxoglutarate/malate carrier protein (36 kDa, Protein from Tetrahymena thermophila SB210)
- Decapping nuclease (10 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt9 (29 kDa, Protein from Tetrahymena thermophila SB210)
- Magnesium ion (24 Da, Ligand)
- Yflt domain-containing protein (19 kDa, Protein from Tetrahymena thermophila SB210)
- Heme-a (852 Da, Ligand)
- Cullin domain-containing protein (8 kDa, Protein from Tetrahymena thermophila SB210)
- Oxoglutarate/malate translocator protein, putative (40 kDa, Protein from Tetrahymena thermophila SB210)
- Nadh dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial (37 kDa, Protein from Tetrahymena thermophila SB210)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Carrier protein (37 kDa, Protein from Tetrahymena thermophila SB210)
- Coxtt27 (23 kDa, Protein from Tetrahymena thermophila SB210)
- Coxbp,chromosome condensation regulator rcc1 repeat protein,chromosome condensation regulator rcc1 repeat protein (58 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf67 (54 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase dimer (complex-iv) from respiratory supercomplex of tetrahymena thermophila (3 MDa, Complex from Tetrahymena thermophila)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Ctf/nf-i domain-containing protein (116 kDa, Protein from Tetrahymena thermophila SB210)
- Ymf70 (10 kDa, Protein from Tetrahymena thermophila SB210)
- Cytochrome c oxidase subunit 2 (72 kDa, Protein from Tetrahymena thermophila SB210)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Surf1-like protein (47 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (20 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (18 kDa, Protein from Tetrahymena thermophila SB210)
- Copper (ii) ion (63 Da, Ligand)
- Transmembrane protein (20 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (26 kDa, Protein from Tetrahymena thermophila SB210)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8b6j
Q-score: 0.402
Muhleip A, Flygaard RK, Baradaran R, Haapanen O, Gruhl T, Tobiasson V, Marechal A, Sharma V, Amunts A
Nature (2023) 615 pp. 934-938 [ DOI: doi:10.1038/s41586-023-05817-y Pubmed: 36949187 ]
- Dimeric cytochrome bc1 complex (complex-iii2) (640 kDa, Complex from Tetrahymena thermophila)
- Cardiolipin (1 kDa, Ligand)
- Peptidase m16 inactive domain protein (58 kDa, Protein from Tetrahymena thermophila SB210)
- Heme c (618 Da, Ligand)
- Uqcrtt3/up1 (5 kDa, Protein from Tetrahymena thermophila SB210)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome protein c1 (37 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (14 kDa, Protein from Tetrahymena thermophila SB210)
- Transmembrane protein, putative (7 kDa, Protein from Tetrahymena thermophila SB210)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Transmembrane protein, putative (15 kDa, Protein from Tetrahymena thermophila SB210)
- Apocytochrome b (50 kDa, Protein from Tetrahymena thermophila SB210)
- Uqcrtt2 (4 kDa, Protein from Tetrahymena thermophila SB210)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Uqcrtt1 (39 kDa, Protein from Tetrahymena thermophila SB210)
- Rieske iron-sulfur protein, ubiquinol-cytochrome c reductase iron-sulfur subunit (30 kDa, Protein from Tetrahymena thermophila SB210)
- M16 family peptidase, putative (53 kDa, Protein from Tetrahymena thermophila SB210)
- Ubiquinol-cytochrome c reductase hinge protein (9 kDa, Protein from Tetrahymena thermophila SB210)
Complex I from E. coli, DDM-purified, with NADH, Resting state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7p61
Q-score: 0.524
Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov L
Nature (2022) 609 pp. 808-814 [ DOI: doi:10.1038/s41586-022-05199-7 Pubmed: 36104567 ]
- Flavin mononucleotide (456 Da, Ligand)
- Proton-translocating nadh-quinone oxidoreductase, chain l (66 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase (99 kDa, Protein from Escherichia coli BL21(DE3))
- Complex i (Complex from Escherichia coli)
- Nadh-quinone oxidoreductase subunit b (25 kDa, Protein from Escherichia coli BL21(DE3))
- 1,4-dihydronicotinamide adenine dinucleotide (665 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (18 kDa, Protein from Escherichia coli BL21(DE3))
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Escherichia coli BL21(DE3))
- Ubiquinone-8 (727 Da, Ligand)
- Nadh dehydrogenase i subunit m (56 kDa, Protein from Escherichia coli BL21(DE3))
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Nadh-quinone oxidoreductase subunit h (36 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase subunit n (52 kDa, Protein from Escherichia coli BL21(DE3))
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit a (16 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase subunit c/d (68 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase subunit i (16 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh dehydrogenase i subunit e (17 kDa, Protein from Escherichia coli BL21(DE3))
- Calcium ion (40 Da, Ligand)
- Nadh-quinone oxidoreductase subunit f (48 kDa, Protein from Escherichia coli BL21(DE3))
Complex I from E. coli, DDM/LMNG-purified, Apo, Open state
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 7p7c
Q-score: 0.65
Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov L
Nature (2022) 609 pp. 808-814 [ Pubmed: 36104567 DOI: doi:10.1038/s41586-022-05199-7 ]
- Nadh-quinone oxidoreductase (99 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Escherichia coli BL21(DE3))
- Eicosane (282 Da, Ligand)
- Nadh-quinone oxidoreductase subunit f (48 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh dehydrogenase i subunit m (56 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase subunit b (25 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase subunit a (16 kDa, Protein from Escherichia coli BL21(DE3))
- Calcium ion (40 Da, Ligand)
- Nadh-quinone oxidoreductase subunit n (52 kDa, Protein from Escherichia coli BL21(DE3))
- Ubiquinone-8 (727 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (17 kDa, Protein from Escherichia coli BL21(DE3))
- Water (18 Da, Ligand)
- Nadh-quinone oxidoreductase subunit h (36 kDa, Protein from Escherichia coli BL21(DE3))
- Nadh-quinone oxidoreductase subunit i (20 kDa, Protein from Escherichia coli BL21(DE3))
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Proton-translocating nadh-quinone oxidoreductase, chain l (66 kDa, Protein from Escherichia coli BL21(DE3))
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Nadh dehydrogenase i subunit e (17 kDa, Protein from Escherichia coli BL21(DE3))
- Flavin mononucleotide (456 Da, Ligand)
- Complex i (Complex from Escherichia coli)
- Nadh-quinone oxidoreductase subunit c/d (68 kDa, Protein from Escherichia coli BL21(DE3))