Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 7vnj
Q-score: 0.536
Kawamoto A, Yamada T, Yoshida T, Sato Y, Kato T, Tsuge H
Nat Commun (2022) 13 pp. 6119-6119 [ Pubmed: 36253419 DOI: doi:10.1038/s41467-022-33888-4 ]
- Cdta-bound cdtb-pore (long) (Complex from Clostridioides difficile)
- Adp-ribosylating binary toxin binding subunit cdtb (75 kDa, Protein from Clostridioides difficile)
- Cdta (Complex)
- Cdtb (Complex from Clostridioides difficile)
- Calcium ion (40 Da, Ligand)
- Adp-ribosyltransferase enzymatic component (49 kDa, Protein from Clostridioides difficile)
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 7vnn
Q-score: 0.529
Kawamoto A, Yamada T, Yoshida T, Sato Y, Kato T, Tsuge H
Nat Commun (2022) 13 pp. 6119-6119 [ Pubmed: 36253419 DOI: doi:10.1038/s41467-022-33888-4 ]
- Cdta-bound cdtb-pore (long) (Complex from Clostridioides difficile)
- Adp-ribosylating binary toxin binding subunit cdtb (75 kDa, Protein from Clostridioides difficile)
- Cdtb-pore (Complex from Clostridioides difficile)
- Cdta (Complex)
- Cdta (49 kDa, Protein from Clostridioides difficile)
- Calcium ion (40 Da, Ligand)
Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xk3
Q-score: 0.567
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 1 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Calcium ion (40 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 2
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xk4
Q-score: 0.562
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 2 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Calcium ion (40 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 3
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xk5
Q-score: 0.546
Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H
Nat Commun (2022) 13 pp. 4082-4082 [ Pubmed: 35882843 DOI: doi:10.1038/s41467-022-31718-1 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Flavin mononucleotide (456 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Calcium ion (40 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 3 (220 kDa, Complex from Vibrio cholerae O395)
Cryo-EM structure of MrgD-Gi complex with beta-alanine
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7y12
Q-score: 0.519
Suzuki S, Iida M, Hiroaki Y, Tanaka K, Kawamoto A, Kato T, Oshima A
Commun Biol (2022) 5 pp. 707-707 [ DOI: doi:10.1038/s42003-022-03668-3 Pubmed: 35840655 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Mus musculus)
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (50 kDa, Protein from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Beta-alanine bound mrgd-gi complex with the scfv16 (Complex from Homo sapiens)
- Beta-alanine (89 Da, Ligand)
- Scfv16 (31 kDa, Protein from synthetic construct)
- G(i) subunit alpha-1,mas-related g-protein coupled receptor member d (Complex from Mus musculus)
- Subunit beta-1,subunit gamma-2 (Complex from synthetic construct)
- Scfv16 (Complex)
Cryo-EM structure of apo-state MrgD-Gi complex (local)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7y13
Q-score: 0.512
Suzuki S, Iida M, Hiroaki Y, Tanaka K, Kawamoto A, Kato T, Oshima A
Commun Biol (2022) 5 pp. 707-707 [ DOI: doi:10.1038/s42003-022-03668-3 Pubmed: 35840655 ]
- Palmitic acid (256 Da, Ligand)
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (50 kDa, Protein from Homo sapiens)
Cryo-EM structure of MrgD-Gi complex with beta-alanine (local)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7y14
Q-score: 0.494
Suzuki S, Iida M, Hiroaki Y, Tanaka K, Kawamoto A, Kato T, Oshima A
Commun Biol (2022) 5 pp. 707-707 [ DOI: doi:10.1038/s42003-022-03668-3 Pubmed: 35840655 ]
- Palmitic acid (256 Da, Ligand)
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (50 kDa, Protein from Homo sapiens)
- Beta-alanine bound mrgd-gi complex with the scfv16 (Complex from Homo sapiens)
- Beta-alanine (89 Da, Ligand)
Cryo-EM structure of apo-state MrgD-Gi complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7y15
Q-score: 0.552
Suzuki S, Iida M, Hiroaki Y, Tanaka K, Kawamoto A, Kato T, Oshima A
Commun Biol (2022) 5 pp. 707-707 [ DOI: doi:10.1038/s42003-022-03668-3 Pubmed: 35840655 ]
- Mrgd-gi complex with the scfv16 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Mus musculus)
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (50 kDa, Protein from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Scfv16 (31 kDa, Protein from synthetic construct)
- G(i) subunit alpha-1,mas-related g-protein coupled receptor member d (Complex from Mus musculus)
- Subunit beta-1,subunit gamma-2 (Complex from synthetic construct)
- Scfv16 (Complex)
Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A Resolution
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6lu1
Q-score: 0.582
Coruh O, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G
Commun Biol (2021) 4 pp. 304-304 [ Pubmed: 33686186 DOI: doi:10.1038/s42003-021-01808-9 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Phylloquinone (450 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Cyanobacterial psi monomer from t. elongatus (350 MDa, Complex from Thermosynechococcus elongatus BP-1)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Chlorophyll a (893 Da, Ligand)