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, Raia P, Koehl A, Laeremans T, Steyaert J, Manglik A, Ballet S, Boland A, Stoeber M
bioRxiv (2023) [ Pubmed: 38106026 DOI: doi:10.1101/2023.12.06.570395 ]
- Nabfab hc (28 kDa, Protein from synthetic construct)
- Nabfab lc (25 kDa, Protein from synthetic construct)
- Mu-type opioid receptor (53 kDa, Protein from Mus musculus)
- Nanobody e (nbe) (18 kDa, Protein from Lama glama)
- Anti-fab nanobody (17 kDa, Protein from Lama glama)
- Mor-nbe-nabfab-antifab complex (120 kDa, Complex from Mus musculus)
PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8qu8
Q-score: 0.306
Popow J, Farnaby W, Gollner A, Kofink C, Fischer G, Wurm M, Zollman D, Wijaya A, Mischerikow N, Hasenoehrl C, Prokofeva P, Arnhof H, Arce-Solano S, Bell S, Boeck G, Diers E, Frost A, Goodwin-Tindall J, Karolyi-Oezguer J, Khan S, Klawatsch T, Koegl M, Kousek R, Kratochvil B, Kropatsch K, Lauber A, McLennan R, Olt S, Peter D, Petermann O, Roessler V, Stolt-Bergner P, Strack P, Strauss E, Trainor N, Vetma V, Whitworth C, Zhong S, Quant J, Weinstabl H, Kuster B, Ettmayer P, Ciulli A
bioRxiv (2023) [ DOI: doi:10.1101/2023.10.24.563163 ]
- Cullin-2 (86 kDa, Protein from Homo sapiens)
- Kras/acbi3/vhl/elob/eloc/cul2/rbx1 (168 kDa, Complex from Homo sapiens)
- Gtpase kras (19 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (12 kDa, Protein from Homo sapiens)
- Von hippel-lindau disease tumor suppressor (24 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- (2s,4r)-1-[(2s)-2-[4-[4-[(3s)-4-[4-[5-[(4s)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5h-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-n-[(1r)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide (1 kDa, Ligand)
- Zinc ion (65 Da, Ligand)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Monomeric E6AP-E6-p53 ternary complex
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 8r1f
Q-score: 0.316
Sandate CR, Chakraborty D, Kater L, Kempf G, Thoma NH
bioRxiv (2023) [ DOI: doi:10.1101/2023.11.01.565136 ]
- Ubiquitin-like protein smt3,protein e6 (31 kDa, Protein from Human papillomavirus type 16)
- Zinc ion (65 Da, Ligand)
- Cellular tumor antigen p53 (46 kDa, Protein from Homo sapiens)
- Ubiquitin-protein ligase e3a (103 kDa, Protein from Homo sapiens)
- Monomeric e6ap-e6-p53 ternary complex (176 kDa, Complex from Homo sapiens)
CryoEM structure of designed modular protein oligomer C8-71
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8f6q
Q-score: 0.423
Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An SJ, Favor A, Ehnes D, Li Z, Praetorius F, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D
bioRxiv (2023) [ DOI: doi:10.1101/2023.03.14.532666 Pubmed: 36993355 ]
CryoEM structure of designed modular protein oligomer C6-79
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8f6r
Q-score: 0.35
Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry CE, Schweppe DK, Freedman BS, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D
Cell (2024) [ DOI: doi:10.1016/j.cell.2024.05.025 Pubmed: 38861993 ]
Porcine epidemic diarrhea virus complete core polymerase complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8urb
Q-score: 0.49
Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN
bioRxiv (2023) [ DOI: doi:10.1101/2023.03.15.532841 Pubmed: 36993498 ]
- Core polymerase complex of the porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short rna substrate (185 kDa, Complex from Porcine epidemic diarrhea virus)
- Nsp8 (21 kDa, Protein from Porcine epidemic diarrhea virus)
- Rna (55-mer) (17 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Nsp7 (9 kDa, Protein from Porcine epidemic diarrhea virus)
- Nsp12 (108 kDa, Protein from Porcine epidemic diarrhea virus)
- Rna (33-mer) (10 kDa, RNA from synthetic construct)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8u4v
Q-score: 0.572
Erramilli SK, Dominik PK, Ogbu CP, Kossiakoff AA, Vecchio AJ
Commun Biol (2024) 7 pp. 733-733 [ Pubmed: 38886509 DOI: doi:10.1038/s42003-024-06437-6 ]
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Claudin-4 (22 kDa, Protein from Homo sapiens)
- Cop-1 sfab light chain (23 kDa, Protein from Homo sapiens)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Water (18 Da, Ligand)
- Heat-labile enterotoxin b chain (14 kDa, Protein from Clostridium perfringens)
- Human claudin-4 complex with clostridium perfringens enterotoxin c-terminal domain, sfab cop-1, and nanobody (100 kDa, Complex from Homo sapiens)
- Cop-1 sfab heavy chain (28 kDa, Protein from Homo sapiens)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8t6j
Q-score: 0.463
Krishna Kumar K, Wang H, Habrian C, Latorraca NR, Xu J, O'Brien ES, Zhang C, Montabana E, Koehl A, Marqusee S, Isacoff EY, Kobilka BK
Nature (2024) 629 pp. 951-956 [ Pubmed: 38632403 DOI: doi:10.1038/s41586-024-07327-x ]
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8t7h
Q-score: 0.43
Krishna Kumar K, Wang H, Habrian C, Latorraca NR, Xu J, O'Brien ES, Zhang C, Montabana E, Koehl A, Marqusee S, Isacoff EY, Kobilka BK
Nature (2024) 629 pp. 951-956 [ DOI: doi:10.1038/s41586-024-07327-x Pubmed: 38632403 ]
- Metabotropic glutamate receptor 5 in complex with quis (Cellular component from Homo sapiens)
- (s)-2-amino-3-(3,5-dioxo-[1,2,4]oxadiazolidin-2-yl)-propionic acid (189 Da, Ligand)
- Nanobody 43 (13 kDa, Protein from Lama glama)
- Metabotropic glutamate receptor 5 (98 kDa, Protein from Homo sapiens)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8t8m
Q-score: 0.493
Krishna Kumar K, Wang H, Habrian C, Latorraca NR, Xu J, O'Brien ES, Zhang C, Montabana E, Koehl A, Marqusee S, Isacoff EY, Kobilka BK
Nature (2024) 629 pp. 951-956 [ DOI: doi:10.1038/s41586-024-07327-x Pubmed: 38632403 ]
- Metabotropic glutamate receptor 5 in complex with quis (Cellular component from Homo sapiens)
- Nb43 (13 kDa, Protein from Lama glama)
- (s)-2-amino-3-(3,5-dioxo-[1,2,4]oxadiazolidin-2-yl)-propionic acid (189 Da, Ligand)
- Metabotropic glutamate receptor 5 (98 kDa, Protein from Homo sapiens)