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RBD of SARS-CoV2 spike protein with ACE2 decoy
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8jje
Q-score: 0.488
Urano E, Itoh Y, Suzuki T, Sasaki T, Kishikawa JI, Akamatsu K, Higuchi Y, Sakai Y, Okamura T, Mitoma S, Sugihara F, Takada A, Kimura M, Nakao S, Hirose M, Sasaki T, Koketsu R, Tsuji S, Yanagida S, Shioda T, Hara E, Matoba S, Matsuura Y, Kanda Y, Arase H, Okada M, Takagi J, Kato T, Hoshino A, Yasutomi Y, Saito A, Okamoto T
Sci Transl Med (2023) 15 pp. eadi2623-eadi2623 [ DOI: doi:10.1126/scitranslmed.adi2623 Pubmed: 37647387 ]
- Sulfate ion (96 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (73 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Spike glycoprotein (138 kDa, Protein from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Ace2 (Complex from Homo sapiens)
- Rbd of sars-cov2 spike protein with ace2 decoy. (460 kDa, Complex)
- Sars-cov2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of the histamine-bound histamine H4 receptor and Gq complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7yfc
Q-score: 0.539
Im D, Kishikawa JI, Shiimura Y, Hisano H, Ito A, Fujita-Fujiharu Y, Sugita Y, Noda T, Kato T, Asada H, Iwata S
Nat Commun (2023) 14 pp. 6538-6538 [ DOI: doi:10.1038/s41467-023-42260-z Pubmed: 37863901 ]
- Histamine h4 receptor (62 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (42 kDa, Protein from Homo sapiens)
- Histamine h4 receptor (Complex)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Mus musculus)
- Scfv16 (Complex from Homo sapiens)
- Engineered g-alpha-q (41 kDa, Protein from Homo sapiens)
- Nb35 (14 kDa, Protein from Lama glama)
- Histamine (111 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Engineered g-alpha-q (Complex from Homo sapiens)
- Histamine-bound histamine h4 receptor in complex with gq (190 kDa, Complex from Homo sapiens)
- Nb35 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Lama glama)
Cryo-EM structure of the imetit-bound histamine H4 receptor and Gq complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7yfd
Q-score: 0.552
Im D, Kishikawa JI, Shiimura Y, Hisano H, Ito A, Fujita-Fujiharu Y, Sugita Y, Noda T, Kato T, Asada H, Iwata S
Nat Commun (2023) 14 pp. 6538-6538 [ DOI: doi:10.1038/s41467-023-42260-z Pubmed: 37863901 ]
- Imetit bound histamine h4 receptor in complex with gq (190 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (42 kDa, Protein from Homo sapiens)
- Nb35 (Complex)
- Scfv16 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Mus musculus)
- Engineered g-alpha-q (41 kDa, Protein from Homo sapiens)
- Nb35 (14 kDa, Protein from Lama glama)
- Cholesterol (386 Da, Ligand)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Engineered g-alpha-q (Complex from Homo sapiens)
- 2-(1~{h}-imidazol-5-yl)ethyl carbamimidothioate (170 Da, Ligand)
- Histamine h4 receptor (Complex from Homo sapiens)
- Histamine h4 receptor (62 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Lama glama)
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 [ DOI: doi:10.1038/s41467-022-31718-1 Pubmed: 35882843 ]
- Flavin mononucleotide (456 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit e (21 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 d (22 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Riboflavin (376 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 [ DOI: doi:10.1038/s41467-022-31718-1 Pubmed: 35882843 ]
- Flavin mononucleotide (456 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 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 d (22 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 2 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Riboflavin (376 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 [ DOI: doi:10.1038/s41467-022-31718-1 Pubmed: 35882843 ]
- Flavin mononucleotide (456 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, state 3 (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Riboflavin (376 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7xk6
Q-score: 0.575
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 [ DOI: doi:10.1038/s41467-022-31718-1 Pubmed: 35882843 ]
- Flavin mononucleotide (456 Da, Ligand)
- Water (18 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, with aurachin d-42 (220 kDa, Complex from Vibrio cholerae O395)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Aurachin d (363 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Riboflavin (376 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7xk7
Q-score: 0.584
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 [ DOI: doi:10.1038/s41467-022-31718-1 Pubmed: 35882843 ]
- Flavin mononucleotide (456 Da, Ligand)
- Water (18 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit e (21 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit d (22 kDa, Protein from Vibrio cholerae O395)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Korormicin (433 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Na(+)-translocating nadh-quinone reductase subunit f (45 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit c (27 kDa, Protein from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit b (45 kDa, Protein from Vibrio cholerae O395)
- Na+-pumping nadh-ubiquinone oxidoreductase from vibrio cholerae, with korormicin (220 kDa, Complex from Vibrio cholerae O395)
- Na(+)-translocating nadh-quinone reductase subunit a (48 kDa, Protein from Vibrio cholerae O395)
- Riboflavin (376 Da, Ligand)
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 [ Pubmed: 35840655 DOI: doi:10.1038/s42003-022-03668-3 ]
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (50 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- G(i) subunit alpha-1,mas-related g-protein coupled receptor member d (Complex from Mus musculus)
- Beta-alanine bound mrgd-gi complex with the scfv16 (Complex from Homo sapiens)
- Subunit beta-1,subunit gamma-2 (Complex from synthetic construct)
- Beta-alanine (89 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Mus musculus)
- Scfv16 (Complex)
- Scfv16 (31 kDa, Protein from synthetic construct)
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 [ Pubmed: 35840655 DOI: doi:10.1038/s42003-022-03668-3 ]
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (Complex from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Soluble cytochrome b562,mas-related g-protein coupled receptor member d (50 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)