The ternary complex of DDB1, DDA1, DET1
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9dhd
Q-score: 0.517
Karayel O, Soung A, Gurung H, Schubert AF, Kschonsak M, Dugger DL, Webster JD, French DM, Klaeger S, Rose CM, Harris SF, Ndoja A, Newton K, Dixit VM
To Be Published
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Det1 homolog (64 kDa, Protein from Homo sapiens)
- Ddb1:dda1:det1 (205 kDa, Complex from Homo sapiens)
- Det1- and ddb1-associated protein 1 (11 kDa, Protein from Homo sapiens)
Structure of an STK19-containing TC-NER complex
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 9bz0
Q-score: 0.448
Mevissen TET, Kummecke M, Schmid EW, Farnung L, Walter JC
Cell (2024) 187 pp. 7091-7106.e24 [ Pubmed: 39547228 DOI: doi:10.1016/j.cell.2024.10.020 ]
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Det1- and ddb1-associated protein 1 (12 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Water (18 Da, Ligand)
- Dna (35-mer) (27 kDa, DNA from synthetic construct)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Transcription-coupled nucleotide excision repair complex (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna (49-mer) (27 kDa, DNA from synthetic construct)
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 ]
- Crebn-ddb1 plus a non-traditional crbn binder (Complex from Homo sapiens)
- (3r)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1h-indazol-3-yl}piperidine-2,6-dione (341 Da, Ligand)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)
- Protein cereblon (53 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
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-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Isoform 1 of inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (31 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Nts (16 kDa, DNA from Homo sapiens)
- Transcription elongation factor 1 homolog (7 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Pol ii-tcr-stk19 (Complex from Homo sapiens)
- Ts (15 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (218 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 rpb9 (14 kDa, Protein from Sus scrofa)
Structure of Pol II-TC-NER-STK19 complex, consensus map
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. 4740-4757.e12 [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Non-template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa domesticus)
- E3 ubiquitin-protein ligase rbx1 (Protein from Homo sapiens)
- Dna-directed rna polymerase subunit rpb7 (Protein from Sus scrofa domesticus)
- Rna (RNA from Homo sapiens)
- Dna excision repair protein ercc-6 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa domesticus)
- Cullin-4a (Protein from Homo sapiens)
- Ternary complex of pol ii-tc-ner-stk19, consensus map (1 MDa, Complex from Homo sapiens)
- Template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (Protein from Sus scrofa domesticus)
- Inactive serine/threonine-protein kinase 19 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa domesticus)
- Nedd8 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (Protein from Homo sapiens)
Structure of Pol II-TC-NER-STK19 complex, focused on CSA-DDB1-DDA1-UVSSA-STK19
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. 4740-4757.e12 [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Inactive serine/threonine-protein kinase 19 (Protein from Homo sapiens)
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Ternary complex of pol ii-tc-ner-stk19, focused on csa-ddb1-dda1-uvssa-stk19 (290 kDa, Complex from Homo sapiens)
Structure of Pol II-TC-NER-STK19 complex, focused on CRL4CSA
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. 4740-4757.e12 [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Nedd8 (Protein from Homo sapiens)
- Ternary complex of pol ii-tc-ner-stk19, focused on crl4csa (300 kDa, Complex from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Cullin-4a (Protein from Homo sapiens)
Structure of Pol II-TC-NER-STK19 complex, focused on CSA-DDB1-DDA1-CSB
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. 4740-4757.e12 [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Ternary complex of pol ii-tc-ner-stk19, focused on csa-ddb1-dda1-csb (360 kDa, Complex from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Template strand dna (DNA from Homo sapiens)
- Dna excision repair protein ercc-6 (Protein from Homo sapiens)
- Non-template strand dna (Protein from Homo sapiens)
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- [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- 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)
- Zinc ion (65 Da, Ligand)
- 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa domesticus)
- Ternary complex of pol ii-tc-ner-stk19, composite map (1 MDa, Complex from Homo sapiens)
- Non-template dna (18 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Rna (8 kDa, RNA from Homo sapiens)
- Dna excision repair protein ercc-8 (45 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
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 [ Pubmed: 39152201 DOI: doi:10.1038/s42004-024-01263-7 ]
- Tyrosine-protein phosphatase non-receptor type 2 (37 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (128 kDa, Protein 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)
- Crbn-ddb1-ptpn2 complex (217 kDa, Complex from Homo sapiens)
- Protein cereblon (51 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)