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
- 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)
- Dna damage-binding protein 1 (129 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 [ DOI: doi:10.1016/j.cell.2024.10.020 Pubmed: 39547228 ]
- Transcription-coupled nucleotide excision repair complex (Complex from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (3 kDa, RNA from synthetic construct)
- Dna (49-mer) (27 kDa, DNA from synthetic construct)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna (35-mer) (27 kDa, DNA from synthetic construct)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Water (18 Da, Ligand)
- Rna polymerase rpb4/rpc9 core domain-containing protein (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)
- Det1- and ddb1-associated protein 1 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
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)
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 [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Dna excision repair protein ercc-6 (Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa domesticus)
- Rna (RNA from Homo sapiens)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa domesticus)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Template strand dna (DNA from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (Protein from Sus scrofa domesticus)
- Ternary complex of pol ii-tc-ner-stk19, consensus map (1 MDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (Protein from Homo sapiens)
- Nedd8 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (Protein from Sus scrofa domesticus)
- Non-template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit rpb7 (Protein from Sus scrofa domesticus)
- Cullin-4a (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa domesticus)
- Inactive serine/threonine-protein kinase 19 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Protein from Sus scrofa domesticus)
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 [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Inactive serine/threonine-protein kinase 19 (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)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein 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 [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (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)
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (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 [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Dna excision repair protein ercc-6 (Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Template strand dna (DNA from Homo sapiens)
- Non-template strand dna (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 damage-binding protein 1 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (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- [ 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)
Llerena Schiffmacher DA, Lee SH, Kliza KW, Theil AF, Akita M, Helfricht A, Bezstarosti K, Gonzalo-Hansen C, van Attikum H, Verlaan-de Vries M, Vertegaal ACO, Hoeijmakers JHJ, Marteijn JA, Lans H, Demmers JAA, Vermeulen M, Sixma TK, Ogi T, Vermeulen W, Pines A
Nat Commun (2024) 15 pp. 6374-6374 [ DOI: doi:10.1038/s41467-024-50584-7 Pubmed: 39075067 ]
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Ternary complex of csa-ddb1-dda1 (190 kDa, Complex from Homo sapiens)
Focused map for CSA-DDB1-DDA1 (map 2)
Llerena Schiffmacher DA, Lee SH, Kliza KW, Theil AF, Akita M, Helfricht A, Bezstarosti K, Gonzalo-Hansen C, van Attikum H, Verlaan-de Vries M, Vertegaal ACO, Hoeijmakers JHJ, Marteijn JA, Lans H, Demmers JAA, Vermeulen M, Sixma TK, Ogi T, Vermeulen W, Pines A
Nat Commun (2024) 15 pp. 6374-6374 [ DOI: doi:10.1038/s41467-024-50584-7 Pubmed: 39075067 ]
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Ternary complex of csa-ddb1-dda1 (190 kDa, Complex from Homo sapiens)