Cryo-EM structure of opioid receptor with biased agonist
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8y45
Q-score: 0.407
Cheng L, Miao Z, Liu S, Li Z, Fu H, Xu C, Hu S, Zhao C, Liu Y, Zhao T, Liu W, Wang H, Liu R, Yan W, Tang X, Liu J, Shao Z, Ke B
Nat Commun (2024) 15 pp. 8284-8284 [ Pubmed: 39333070 DOI: doi:10.1038/s41467-024-52601-1 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-2 (40 kDa, Protein from Homo sapiens)
- Scfv16 (28 kDa, Protein from Mus musculus)
- Delta-type opioid receptor (36 kDa, Protein from Homo sapiens)
- ~{n},~{n}-diethyl-4-(5-oxidanylspiro[chromene-2,4'-piperidine]-4-yl)benzamide (392 Da, Ligand)
- Cryo-em structure of opioid receptor with biased agonist (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 7yhs
Q-score: 0.404
Gao Z, Zhang L, Ge Z, Wang H, Yue Y, Jiang Z, Wang X, Xu C, Zhang Y, Yang M, Feng Y
J Biol Chem (2022) 298 pp. 102575-102575 [ Pubmed: 36209819 DOI: doi:10.1016/j.jbc.2022.102575 ]
- Dna (39-mer) (16 kDa, DNA from Pseudomonas aeruginosa)
- Dna (5'-d(p*ap*gp*cp*ap*gp*cp*tp*gp*cp*ap*cp*c)-3') (16 kDa, DNA from Pseudomonas aeruginosa)
- Dna (Complex)
- Csy-acrif4 (Complex from Pseudomonas aeruginosa)
- Csy4 (21 kDa, Protein from Pseudomonas aeruginosa)
- Type i-f crispr-associated protein csy1 (49 kDa, Protein from Pseudomonas aeruginosa)
- Rna (Complex from Pseudomonas aeruginosa)
- Acrif4 (11 kDa, Protein from Pseudomonas aeruginosa)
- Rna (58-mer) (19 kDa, RNA from Pseudomonas aeruginosa)
- Crispr-associated protein csy3 (37 kDa, Protein from Pseudomonas aeruginosa)
- Crispr type i-f/ypest-associated protein csy2 (36 kDa, Protein from Pseudomonas aeruginosa)
- Csy-acrif4-dsdna (Complex from Pseudomonas aeruginosa)
EV-D68 in complex with 2H12 Fab (state S2)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ebr
Q-score: 0.408
Zhang C, Xu C, Dai W, Wang Y, Liu Z, Zhang X, Wang X, Wang H, Gong S, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 2904-2904 [ DOI: doi:10.1038/s41467-021-23199-5 Pubmed: 34006855 ]
- Capsid protein vp1 (32 kDa, Protein from Human enterovirus D68)
- 2h12 fab heavy chain (22 kDa, Protein from Mus musculus)
- 2h12 fab (Cellular component from Mus musculus)
- Capsid protein vp3 (27 kDa, Protein from Human enterovirus D68)
- Capsid protein vp2 (27 kDa, Protein from Human enterovirus D68)
- 2h12 fab light chain (23 kDa, Protein from Mus musculus)
- Capsid protein vp4 (7 kDa, Protein from Human enterovirus D68)
- Enterovirus d68 (Virus from Enterovirus D68)
- Enterovirus d68 in complex with 2h12 fab (Complex)
EV-D68 in complex with 2H12 Fab (state S1)
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7ebz
Q-score: 0.519
Zhang C, Xu C, Dai W, Wang Y, Liu Z, Zhang X, Wang X, Wang H, Gong S, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 2904-2904 [ DOI: doi:10.1038/s41467-021-23199-5 Pubmed: 34006855 ]
- Capsid protein vp1 (32 kDa, Protein from Human enterovirus D68)
- Capsid protein vp3 (27 kDa, Protein from Human enterovirus D68)
- Capsid protein vp2 (27 kDa, Protein from Human enterovirus D68)
- Fab 2h12 heavy chain (22 kDa, Protein from Mus musculus)
- Fab 2h12 light chain (23 kDa, Protein from Mus musculus)
- Capsid protein vp4 (7 kDa, Protein from Human enterovirus D68)
- Enterovirus d68 (Virus from Enterovirus D68)
- Enterovirus d68 in complex with 2h12 fab (Complex)
- 2h12 fab (Complex from Mus musculus)
EV-D68 in complex with 8F12 Fab
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 7ec5
Q-score: 0.548
Zhang C, Xu C, Dai W, Wang Y, Liu Z, Zhang X, Wang X, Wang H, Gong S, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 2904-2904 [ DOI: doi:10.1038/s41467-021-23199-5 Pubmed: 34006855 ]
- Genome polyprotein (27 kDa, Protein from Human enterovirus D68)
- Capsid protein vp1 (32 kDa, Protein from Human enterovirus D68)
- Capsid protein vp3 (27 kDa, Protein from Human enterovirus D68)
- 8f12 fab heavy chain (23 kDa, Protein from Mus musculus)
- 8f12 fab light chain (23 kDa, Protein from Mus musculus)
- Enterovirus d68 in complex with 8f12 fab (Complex)
- Capsid protein vp4 (7 kDa, Protein from Human enterovirus D68)
- Enterovirus d68 (Virus from Enterovirus D68)
- 8f12 fab (Complex from Mus musculus)
EV-D68 in complex with 2H12 Fab (State 3)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ecy
Q-score: 0.36
Zhang C, Xu C, Dai W, Wang Y, Liu Z, Zhang X, Wang X, Wang H, Gong S, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 2904-2904 [ DOI: doi:10.1038/s41467-021-23199-5 Pubmed: 34006855 ]
- Capsid protein vp1 (32 kDa, Protein from Human enterovirus D68)
- Enterovirus d68 (Complex from Enterovirus D68)
- Capsid protein vp3 (27 kDa, Protein from Human enterovirus D68)
- Capsid protein vp2 (27 kDa, Protein from Human enterovirus D68)
- Fab 2h12 heavy chain (22 kDa, Protein from Mus musculus)
- Fab 2h12 light chain (23 kDa, Protein from Mus musculus)
- Enterovirus d68 in complex with 2h12 fab (Complex)
- 2h12 fab (Complex from Mus musculus)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7dcc
Q-score: 0.137
Zhang C, Wang Y, Zhu Y, Liu C, Gu C, Xu S, Wang Y, Zhou Y, Wang Y, Han W, Hong X, Yang Y, Zhang X, Wang T, Xu C, Hong Q, Wang S, Zhao Q, Qiao W, Zang J, Kong L, Wang F, Wang H, Qu D, Lavillette D, Tang H, Deng Q, Xie Y, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 264-264 [ DOI: doi:10.1038/s41467-020-20465-w Pubmed: 33431876 ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- The light chain of 3c1 fab (23 kDa, Protein from Mus musculus)
- Complex of sarc-cov2-s protein with 3c1 fab, all the three rbds are in the up conformation and each of them associates with a 3c1 fab (Complex from Mus musculus)
- 3c1 fab with a heavy chain and a light chain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sarc-cov2-s protein (Complex)
- The heavy chain of 3c1 fab (24 kDa, Protein from Mus musculus)
S-3C1-F3a structure, two RBDs are up and one RBD is down, each RBD binds with a 3C1 fab.
Resolution: 5.9 Å
EM Method: Single-particle
Fitted PDBs: 7dcx
Q-score: 0.087
Zhang C, Wang Y, Zhu Y, Liu C, Gu C, Xu S, Wang Y, Zhou Y, Wang Y, Han W, Hong X, Yang Y, Zhang X, Wang T, Xu C, Hong Q, Wang S, Zhao Q, Qiao W, Zang J, Kong L, Wang F, Wang H, Qu D, Lavillette D, Tang H, Deng Q, Xie Y, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 264-264 [ DOI: doi:10.1038/s41467-020-20465-w Pubmed: 33431876 ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- The light chain of 3c1 fab (23 kDa, Protein from Mus musculus)
- Sars-cov2-s protein (Complex)
- Complex of sars-cov2-s protein with 3c1 fab, two rbds are up and one rbd is down (Complex from Mus musculus)
- The heavy chain of 3c1 fab that binds with the up rbd (24 kDa, Protein from Mus musculus)
- 3c1 fab with a heavy chain and a light chain (Complex from Severe acute respiratory syndrome coronavirus 2)
S-3C1-F2 structure, two RBDs are up and one RBD is down, the two up RBD bind with a 3C1 fab.
Resolution: 5.6 Å
EM Method: Single-particle
Fitted PDBs: 7dd2
Q-score: 0.1
Zhang C, Wang Y, Zhu Y, Liu C, Gu C, Xu S, Wang Y, Zhou Y, Wang Y, Han W, Hong X, Yang Y, Zhang X, Wang T, Xu C, Hong Q, Wang S, Zhao Q, Qiao W, Zang J, Kong L, Wang F, Wang H, Qu D, Lavillette D, Tang H, Deng Q, Xie Y, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 264-264 [ DOI: doi:10.1038/s41467-020-20465-w Pubmed: 33431876 ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- The light chain of 3c1 fab (23 kDa, Protein from Mus musculus)
- Sars-cov2-s protein (Complex from Mus musculus)
- The heavy chain of 3c1 fab (24 kDa, Protein from Mus musculus)
- 3c1 fab with a heavy chain and a light chain (Complex)
- Complex of sars-cov2-s protein with 3c1 fab, two rbds are up and one rbd is down, only the two up rbds bind with a 3c1 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
S-3C1-F1 structure, one RBD is up and two RBDs are down, the up RBD binds with a 3C1 fab
Resolution: 7.5 Å
EM Method: Single-particle
Fitted PDBs: 7dd8
Q-score: 0.081
Zhang C, Wang Y, Zhu Y, Liu C, Gu C, Xu S, Wang Y, Zhou Y, Wang Y, Han W, Hong X, Yang Y, Zhang X, Wang T, Xu C, Hong Q, Wang S, Zhao Q, Qiao W, Zang J, Kong L, Wang F, Wang H, Qu D, Lavillette D, Tang H, Deng Q, Xie Y, Cong Y, Huang Z
Nat Commun (2021) 12 pp. 264-264 [ DOI: doi:10.1038/s41467-020-20465-w Pubmed: 33431876 ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov2-s protein (Complex)
- Complex of sars-cov2-s protein with 3c1 fab, one rbd is up and two rbds are down, the up rbd binds with a 3c1 fab (Complex from Mus musculus)
- The light chain of 3c1 chain (23 kDa, Protein from Mus musculus)
- 3c1 fab with a heavy chain and a light chain (Complex from Severe acute respiratory syndrome coronavirus 2)
- The heavy chain of 3c1 fab (24 kDa, Protein from Mus musculus)