The cryo-EM structure of TdpAB in complex with AMPPNP and PT-DNA
An T, Tan Q, Jiang L, Liu L, Jiang X, Liu L, Chang X, Tian X, Deng Z, Gao S, Wang L, Chen S
Nat Chem Biol (2025) [ Pubmed: 39820821 DOI: doi:10.1038/s41589-024-01832-w ]
- Tdpa (66 kDa, Protein from Thermus antranikianii DSM 12462)
- Tdpb (42 kDa, Protein from Thermus antranikianii DSM 12462)
- Tdpab in complex with amppnp and pt-dna (Complex from Thermus antranikianii DSM 12462)
- Dna (5'-d(p*tp*tp*gp*cp*ap*ap*ap*ap*gp*gp*gp*c)-3') (3 kDa, DNA from Thermus antranikianii DSM 12462)
- Dna (5'-d(p*gp*cp*cp*cp*tp*tp*tp*tp*gp*cp*ap*a)-3') (3 kDa, DNA from Thermus antranikianii DSM 12462)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
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)
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 8tpw
Q-score: 0.423
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 ]
- Antibody fragment 1b2, light chain (25 kDa, Protein from Homo sapiens)
- Antibody fragment 1b2, heavy chain (26 kDa, Protein from Homo sapiens)
- Eryaii,eryaii,eryaii,eryaii,6-deoxyerythronolide-b synthase erya3, modules 5 and 6 (186 kDa, Protein from Saccharopolyspora erythraea)
- Crosslinked debs module 3 in complex with antibody fragment 1b2 (420 kDa, Complex from Saccharopolyspora erythraea)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8tpx
Q-score: 0.396
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 ]
- Antibody fragment 1b2, light chain (25 kDa, Protein from Homo sapiens)
- Antibody fragment 1b2, heavy chain (26 kDa, Protein from Homo sapiens)
- Eryaii,eryaii,eryaii,6-deoxyerythronolide-b synthase erya3, modules 5 and 6 (186 kDa, Protein from Saccharopolyspora erythraea)
- Crosslinked debs module 3 in complex with antibody fragment 1b2 (420 kDa, Complex from Saccharopolyspora erythraea)
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: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 8tjn
Q-score: 0.364
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 ]
- Crosslinked debs module 1 in complex with antibody fragment 1b2 (480 kDa, Complex from Saccharopolyspora erythraea)
- Antibody fragment 1b2, heavy chain (26 kDa, Protein from Homo sapiens)
- Eryai,6-deoxyerythronolide-b synthase erya3, modules 5 and 6 (188 kDa, Protein from Saccharopolyspora erythraea)
- Antibody fragment 1b2, light chain (25 kDa, Protein from Homo sapiens)
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 8tjo
Q-score: 0.365
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 ]
- Crosslinked debs module 1 in complex with antibody fragment 1b2 (480 kDa, Complex from Saccharopolyspora erythraea)
- Antibody fragment 1b2, heavy chain (26 kDa, Protein from Homo sapiens)
- Eryai,6-deoxyerythronolide-b synthase erya3, modules 5 and 6 (188 kDa, Protein from Saccharopolyspora erythraea)
- Antibody fragment 1b2, light chain (25 kDa, Protein from Homo sapiens)