cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9dqd
Q-score: 0.467
Lejava A, Miseo GA, Phan T, Zhu J, Powers HL, Li J, Mortensen DS, Zapf CW, Khambatta G, Buenviaje J, Holmberg-Douglas N
Acs Med.Chem.Lett. (2025) 16 pp. 89-95 [ Pubmed: 39811117 DOI: doi:10.1021/acsmedchemlett.4c00462 ]
- Zinc ion (65 Da, Ligand)
- (3r)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1h-indazol-3-yl}piperidine-2,6-dione (341 Da, Ligand)
- Crebn-ddb1 plus a non-traditional crbn binder (Complex from Homo sapiens)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)
- Protein cereblon (53 kDa, Protein from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9er2
Q-score: 0.448
van den Heuvel D, Rodriguez-Martinez M, van der Meer PJ, Nieto Moreno N, Park J, Kim HS, van Schie JJM, Wondergem AP, D'Souza A, Yakoub G, Herlihy AE, Kashyap K, Boissiere T, Walker J, Mitter R, Apelt K, de Lint K, Kirdok I, Ljungman M, Wolthuis RMF, Cramer P, Scharer OD, Kokic G, Svejstrup JQ, Luijsterburg MS
Cell (2024) 187 pp. 7107- [ DOI: doi:10.1016/j.cell.2024.10.018 Pubmed: 39547229 ]
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Ts (15 kDa, DNA from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Pol ii-tcr-stk19 (Complex from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Isoform 1 of inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor 1 homolog (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*cp*ap*ap*ap*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (4 kDa, RNA from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
Structure of Pol II-TC-NER-STK19 complex, composite map
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9fd2
Q-score: 0.436
Ramadhin AR, Lee SH, Zhou D, Salmazo A, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA
Mol Cell (2024) 84 pp. 4740- [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Non-template dna (18 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Ternary complex of pol ii-tc-ner-stk19, composite map (1 MDa, Complex from Homo sapiens)
- Det1- and ddb1-associated protein 1 (16 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (82 kDa, Protein from Homo sapiens)
- Rna polymerase ii, i and iii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa domesticus)
- Rna (8 kDa, RNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Template dna (18 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
Degrader-induced complex between PTPN2 and CRBN-DDB1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8uh6
Q-score: 0.266
Hao Q, Rathinaswamy MK, Klinge KL, Bratkowski M, Mafi A, Baumgartner CK, Hamel KM, Veits GK, Jain R, Catalano C, Fitzgerald M, Hird AW, Park E, Vora HU, Henderson JA, Longenecker K, Hutchins CW, Qiu W, Scapin G, Sun Q, Stoll VS, Sun C, Li P, Eaton D, Stokoe D, Fisher SL, Nasveschuk CG, Paddock M, Kort ME
Commun Chem (2024) 7 pp. 183-183 [ DOI: doi:10.1038/s42004-024-01263-7 Pubmed: 39152201 ]
- Zinc ion (65 Da, Ligand)
- Protein cereblon (51 kDa, Protein from Homo sapiens)
- Crbn-ddb1-ptpn2 complex (217 kDa, Complex from Homo sapiens)
- (5p)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4s)-1-({3-[(4-{1-[(3r)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1h-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid (976 Da, Ligand)
- Tyrosine-protein phosphatase non-receptor type 2 (37 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (128 kDa, Protein from Homo sapiens)
Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8tnp
Q-score: 0.507
Mercer JAM, DeCarlo SJ, Roy Burman SS, Sreekanth V, Nelson AT, Hunkeler M, Chen PJ, Donovan KA, Kokkonda P, Tiwari PK, Shoba VM, Deb A, Choudhary A, Fischer ES, Liu DR
Science (2024) 383 pp. eadk4422-eadk4422 [ DOI: doi:10.1126/science.adk4422 Pubmed: 38484051 ]
- Zinc ion (65 Da, Ligand)
- Protein cereblon (55 kDa, Protein from Homo sapiens)
- S-pomalidomide (273 Da, Ligand)
- Dna damage-binding protein 1 (96 kDa, Protein from Homo sapiens)
- Maltose/maltodextrin-binding periplasmic protein,sd40 (50 kDa, Protein from Homo sapiens)
- Ternary complex of ddb1db:crbn:pomalidomide with sd40 (201 kDa, Complex)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8b3f
Q-score: 0.456
To Be Published
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Ts (15 kDa, DNA from Homo sapiens)
- Pol ii-csb-csa-ddb1-elof1 complex. (Complex from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Rna (3 kDa, RNA from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8b3i
Q-score: 0.466
To Be Published
- Cullin-4a (87 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d2 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- C(n)rl4csa-e2-ub complex. (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and rat STAT2 CCD
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 7zn7
Q-score: 0.395
Le-Trilling VTK, Banchenko S, Paydar D, Leipe PM, Binting L, Lauer S, Graziadei A, Klingen R, Gotthold C, Burger J, Bracht T, Sitek B, Jan Lebbink R, Malyshkina A, Mielke T, Rappsilber J, Spahn CM, Voigt S, Trilling M, Schwefel D
EMBO J (2023) 42 pp. e112351-e112351 [ Pubmed: 36762436 DOI: doi:10.15252/embj.2022112351 ]
- E27 (Complex from Murid betaherpesvirus 8)
- Zinc ion (65 Da, Ligand)
- Signal transducer and activator of transcription (Complex from Rattus norvegicus)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)
- B27a (76 kDa, Protein from Murid betaherpesvirus 8)
- Signal transducer and activator of transcription (97 kDa, Protein from Rattus norvegicus)
- Dna damage-binding protein 1 (Complex from Homo sapiens)
- Ternary complex of rcmv-e e27 with human ddb1 (deltabpb) and rat stat2 (100 kDa, Complex from Murid betaherpesvirus 8)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8cvp
Q-score: 0.465
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Zinc ion (65 Da, Ligand)
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Cereblon~ddb1 in the apo form (177 kDa, Complex from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d7u
Q-score: 0.515
Watson ER, Novick S, Matyskiela ME, Chamberlain PP, H de la Pena A, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC
Science (2022) 378 pp. 549-553 [ Pubmed: 36378961 DOI: doi:10.1126/science.add7574 ]
- Zinc ion (65 Da, Ligand)
- Mezigdomide (567 Da, Ligand)
- Protein cereblon (50 kDa, Protein from Homo sapiens)
- Cereblon~ddb1 bound to cc-92480 with ddb1 in the linear conformation (177 kDa, Complex from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)