C(N)RL4CSA-UVSSA-E2-ubiquitin complex.
Kokic G, Yakoub G, van den Heuvel D, Wondergem AP, van der Meer PJ, van der Weegen Y, Chernev A, Fianu I, Fokkens TJ, Lorenz S, Urlaub H, Cramer P, Luijsterburg MS
Nat Struct Mol Biol (2024) 31 pp. 536-547 [ Pubmed: 38316879 DOI: doi:10.1038/s41594-023-01207-0 ]
- Cullin-4a (87 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d2 isoform x3 (16 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- C(n)rl4csa-uvssa-e2-ubiquitin complex. (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7oob
Q-score: 0.566
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Ts (14 kDa, DNA from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (3 kDa, RNA from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Complex between the transcribing rna polymerase ii and tcr factors in the presence of adp-bef3. (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna excision repair protein ercc-6 and ercc-8, dna damage-binding protein 1 (Complex from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opc
Q-score: 0.472
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Ts (14 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Supplementary proteins (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- 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)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to csb, crl4csa, uvssa, paf and spt6. (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 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)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
Pol II-CSB-CSA-DDB1-UVSSA (Structure1)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7oo3
Q-score: 0.521
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna repair proteins, csb element and scaffold protein (Complex from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- 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)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna polymerase ii elongation complex with csb, csa-ddb1 and uvssa. (Complex)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Rna (3 kDa, RNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Nts, ts & rna (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna directed rna polymerase (Complex from Sus scrofa)
- Csb element (2 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7oop
Q-score: 0.421
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Ts (14 kDa, DNA from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog (133 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Supplementory proteins (Complex from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Complex between transcribing pol ii, tcr factors and elongation factors spt6 and paf. (Complex)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- 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)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- 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)
- Magnesium ion (24 Da, Ligand)
- 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)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opd
Q-score: 0.472
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to trc factors, spt6 and paf. (Complex)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Ts (14 kDa, DNA from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- 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 polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Supplementary proteins (Complex from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)