Structure of the mu opioid receptor bound to the antagonist nanobody NbE
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8qot
Q-score: 0.413
Yu J, Kumar A, Zhang X, Martin C, Van Holsbeeck K, Raia P, Koehl A, Laeremans T, Steyaert J, Manglik A, Ballet S, Boland A, Stoeber M
Nat Commun (2024) 15 pp. 8687-8687 [ Pubmed: 39384768 DOI: doi:10.1038/s41467-024-52947-6 ]
- Nabfab hc (28 kDa, Protein from synthetic construct)
- Anti-fab nanobody (17 kDa, Protein from Lama glama)
- Nanobody e (nbe) (18 kDa, Protein from Lama glama)
- Mor-nbe-nabfab-antifab complex (120 kDa, Complex from Mus musculus)
- Mu-type opioid receptor (53 kDa, Protein from Mus musculus)
- Nabfab lc (25 kDa, Protein from synthetic construct)
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7yud
Q-score: 0.53
Duan Y, Leong NCP, Zhao J, Zhang Y, Nguyen DT, Ha HTT, Wang N, Xia R, Xu Z, Ma Z, Qian Y, Yin H, Zhu X, Zhang A, Guo C, Xia Y, Nguyen LN, He Y
Cell Res (2024) 34 pp. 177-180 [ DOI: doi:10.1038/s41422-023-00913-0 Pubmed: 38123825 ]
- Nbfab-h-chain (26 kDa, Protein from synthetic construct)
- Tc-nb8 (14 kDa, Protein from Lama glama)
- Anti-fab nanobody (13 kDa, Protein from Lama glama)
- Spns2 nanobody complex (Complex from Lama glama)
- (2~{s})-2-azanyl-4-(4-octylphenyl)-2-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]butan-1-ol (387 Da, Ligand)
- Sphingosine-1-phosphate transporter spns2 (58 kDa, Protein from Homo sapiens)
- Nbfab l-chain (23 kDa, Protein from synthetic construct)
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 7yuf
Q-score: 0.458
Duan Y, Leong NCP, Zhao J, Zhang Y, Nguyen DT, Ha HTT, Wang N, Xia R, Xu Z, Ma Z, Qian Y, Yin H, Zhu X, Zhang A, Guo C, Xia Y, Nguyen LN, He Y
Cell Res (2024) 34 pp. 177-180 [ DOI: doi:10.1038/s41422-023-00913-0 Pubmed: 38123825 ]
- Antifab nanobody (13 kDa, Protein from Lama glama)
- Tc-nb8 (14 kDa, Protein from Lama glama)
- Spns2 nanobody complex (Complex from Lama glama)
- Nbfab h-chain (26 kDa, Protein from synthetic construct)
- Sphingosine-1-phosphate transporter spns2 (58 kDa, Protein from Homo sapiens)
- Nbfab l-chain (23 kDa, Protein from synthetic construct)
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 7zlg
Q-score: 0.454
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Synthetic octapeptide wehi 1886493 (821 Da, Protein from synthetic construct)
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase cedpy19, in complex with acceptor peptide and bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 7zlh
Q-score: 0.455
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in apo state, bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 7zli
Q-score: 0.496
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in complex with dol25-p-man and bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] [(3~{s},6~{z},10~{e},14~{e})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] hydrogen phosphate (602 Da, Ligand)
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 7zlj
Q-score: 0.411
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in ternary complex with dol25-p-c-man and acceptor peptide, bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- Synthetic octapeptide wehi 1886493 (821 Da, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
- [(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl-[(3~{s},6~{e},10~{z},14~{e})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphinic acid (600 Da, Ligand)