Kappa opioid receptor:Galphai protein in complex with inverse agonist norBNI
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vve
Q-score: 0.333
Tyson AS, Khan S, Motiwala Z, Han GW, Zhang Z, Ranjbar M, Styrpejko D, Ramos-Gonzalez N, Woo S, Villers K, Landaker D, Kenakin T, Shenvi R, Majumdar S, Gati C
Nat Chem Biol (2025) [ Pubmed: 39775170 DOI: doi:10.1038/s41589-024-01812-0 ]
- Scfv16 (26 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 (37 kDa, Protein from Homo sapiens)
- Kappa-type opioid receptor (42 kDa, Protein from Homo sapiens)
- Kappa opioid receptor in complex with heterotrimeric g protein (gai/b/g) and inverse agonist norbni (130 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- (4bs,8r,8as,10as,11r,14as,19ar,20br)-7,12-bis(cyclopropylmethyl)-5,6,7,8,9,10,11,12,13,14,20,20b-dodecahydro-19ah-4,8:11,15-dimethanobis[1]benzofuro[2,3-a:3',2'-i]dipyrido[4,3-b:3',4'-h]carbazole-1,8a,10a,18-tetrol (661 Da, Ligand)
Kappa opioid receptor:Galphai protein in complex with inverse agonist JDTic
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8vvf
Q-score: 0.428
Tyson AS, Khan S, Motiwala Z, Han GW, Zhang Z, Ranjbar M, Styrpejko D, Ramos-Gonzalez N, Woo S, Villers K, Landaker D, Kenakin T, Shenvi R, Majumdar S, Gati C
Nat Chem Biol (2025) [ Pubmed: 39775170 DOI: doi:10.1038/s41589-024-01812-0 ]
- Scfv16 (26 kDa, Protein from Mus musculus)
- (3r)-7-hydroxy-n-{(2s)-1-[(3r,4r)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide (465 Da, Ligand)
- 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 (37 kDa, Protein from Homo sapiens)
- Kappa-type opioid receptor (42 kDa, Protein from Homo sapiens)
- Kappa opioid receptor in complex with heterotrimeric g protein (gai/b/g) and inverse agonist jdtic (130 MDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
Kappa opioid receptor in complex with heterotrimerig Gi protein, bound to inverse agonist GB18
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vvg
Q-score: 0.386
Tyson AS, Khan S, Motiwala Z, Han GW, Zhang Z, Ranjbar M, Styrpejko D, Ramos-Gonzalez N, Woo S, Villers K, Landaker D, Kenakin T, Shenvi R, Majumdar S, Gati C
Nat Chem Biol (2025) [ Pubmed: 39775170 DOI: doi:10.1038/s41589-024-01812-0 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Kappa-type opioid receptor (42 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Kappa opioid receptor in complex with heterotrimeric g protein (gai/b/g) and inverse agonist jdtic (130 MDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Methyl (2s,3r,3as,4s,5as,9as,9bs)-3-methyl-2-[(2s,6s)-6-methylpiperidin-2-yl]dodecahydro-3,5a-epoxycyclopenta[a]naphthalene-4-carboxylate (361 Da, Ligand)
- Scfv16 (26 kDa, Protein from Homo sapiens)
Kappa opioid receptor:Galphai protein in complex with inverse agonist JDTic , no scFv16
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 9d61
Q-score: 0.312
Tyson AS, Khan S, Motiwala Z, Han GW, Zhang Z, Ranjbar M, Styrpejko D, Ramos-Gonzalez N, Woo S, Villers K, Landaker D, Kenakin T, Shenvi R, Majumdar S, Gati C
Nat Chem Biol (2025) [ Pubmed: 39775170 DOI: doi:10.1038/s41589-024-01812-0 ]
- (3r)-7-hydroxy-n-{(2s)-1-[(3r,4r)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide (465 Da, Ligand)
- 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 (37 kDa, Protein from Homo sapiens)
- Kappa-type opioid receptor (42 kDa, Protein from Homo sapiens)
- Kappa opioid receptor in complex with heterotrimeric g protein (gai/b/g) and inverse agonist jdtic (130 MDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
HER2 S310F in complex with TL1 Fab
Resolution: 2.61 Å
EM Method: Single-particle
Fitted PDBs: 8vqd
Q-score: 0.6
Bang I, Hattori T, Leloup N, Corrado A, Nyamaa A, Koide A, Geles K, Buck E, Koide S
Nat Chem Biol (2024) [ Pubmed: 39438724 DOI: doi:10.1038/s41589-024-01751-w ]
- Variable heavy chain of tl1 fab (27 kDa, Protein from Homo sapiens)
- Her2 s310f in complex with tl1 fab (150 MDa, Complex from Homo sapiens)
- Receptor tyrosine-protein kinase erbb-2/higg1 fc domain fusion (99 kDa, Protein from Homo sapiens)
- Variable light chain of tl1 fab (23 kDa, Protein from Homo sapiens)
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8tko
Q-score: 0.493
Cogan DP, Soohoo AM, Chen M, Liu Y, Brodsky KL, Khosla C
Nat Chem Biol (2024) [ Pubmed: 39179672 DOI: doi:10.1038/s41589-024-01709-y ]
- Eryai (20 kDa, Protein from Saccharopolyspora erythraea)
- Ks-at core of debs module 3 crosslinked with its translocation acp partner of module 2 (220 kDa, Complex from Saccharopolyspora erythraea)
- Eryaii (99 kDa, Protein from Saccharopolyspora erythraea)
Resolution: 3.71 Å
EM Method: Single-particle
Fitted PDBs: 8tjp
Q-score: 0.388
Cogan DP, Soohoo AM, Chen M, Liu Y, Brodsky KL, Khosla C
Nat Chem Biol (2024) [ Pubmed: 39179672 DOI: doi:10.1038/s41589-024-01709-y ]
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8rb8
Q-score: 0.455
Nat Chem Biol (2024) 20 pp. 1078-1085 [ Pubmed: 38890433 DOI: doi:10.1038/s41589-024-01641-1 ]
- Ion-translocating oxidoreductase complex subunit c (52 kDa, Protein from Azotobacter vinelandii DJ)
- Ion-translocating oxidoreductase complex subunit g (25 kDa, Protein from Azotobacter vinelandii DJ)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Ion-translocating oxidoreductase complex subunit a (19 kDa, Protein from Azotobacter vinelandii DJ)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Ion-translocating oxidoreductase complex subunit b (17 kDa, Protein from Azotobacter vinelandii DJ)
- Flavin mononucleotide (456 Da, Ligand from Azotobacter vinelandii DJ)
- Ion-translocating oxidoreductase complex subunit d (39 kDa, Protein from Azotobacter vinelandii DJ)
- Iron/sulfur cluster (351 Da, Ligand)
- Protein rnfh (9 kDa, Protein from Azotobacter vinelandii DJ)
- Heptameric complex nadh:ferredoxin oxidoreductase rnf1 (188 kDa, Complex from Azotobacter vinelandii DJ)
- Ion-translocating oxidoreductase complex subunit e (25 kDa, Protein from Azotobacter vinelandii DJ)
Cryo-EM structure of the NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii, NADH added
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8rb9
Q-score: 0.491
Nat Chem Biol (2024) 20 pp. 1078-1085 [ Pubmed: 38890433 DOI: doi:10.1038/s41589-024-01641-1 ]
- Ion-translocating oxidoreductase complex subunit c (52 kDa, Protein from Azotobacter vinelandii DJ)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Riboflavin (376 Da, Ligand)
- Ion-translocating oxidoreductase complex subunit a (19 kDa, Protein from Azotobacter vinelandii DJ)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Ion-translocating oxidoreductase complex subunit b (17 kDa, Protein from Azotobacter vinelandii DJ)
- Ion-translocating oxidoreductase complex subunit g (24 kDa, Protein from Azotobacter vinelandii DJ)
- Flavin mononucleotide (456 Da, Ligand from Azotobacter vinelandii DJ)
- Ion-translocating oxidoreductase complex subunit d (39 kDa, Protein from Azotobacter vinelandii DJ)
- Iron/sulfur cluster (351 Da, Ligand)
- Protein rnfh (9 kDa, Protein from Azotobacter vinelandii DJ)
- Heptameric complex nadh:ferredoxin oxidoreductase rnf1 (188 kDa, Complex from Azotobacter vinelandii DJ)
- Ion-translocating oxidoreductase complex subunit e (25 kDa, Protein from Azotobacter vinelandii DJ)