Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7unc
Q-score: 0.344
Filipovski M, Soffers JHM, Vos SM, Farnung L
Science (2022) 376 pp. 1313-1316 [ Pubmed: 35709268 DOI: doi:10.1126/science.abo3851 ]
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Pol ii-dsif-spt6-paf1c-tfiis complex with rewrapped nucleosome (Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- Dna-directed rna polymerase subunit (219 kDa, Protein from pig)
- Rpb8 (17 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- Rna (5 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from pig)
- Rpol4c domain-containing protein (20 kDa, Protein from pig)
- Template dna (66 kDa, DNA from synthetic construct)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Non-template dna (64 kDa, DNA from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from pig)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7und
Q-score: 0.216
Filipovski M, Soffers JHM, Vos SM, Farnung L
Science (2022) 376 pp. 1313-1316 [ Pubmed: 35709268 DOI: doi:10.1126/science.abo3851 ]
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- Dna-directed rna polymerase subunit (219 kDa, Protein from pig)
- Rpb8 (17 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Rna (5 kDa, RNA from synthetic construct)
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- Pol ii-dsif-spt6-paf1c-tfiis complex (stalled at +38) (Complex)
- Zinc ion (65 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from pig)
- Rpol4c domain-containing protein (20 kDa, Protein from pig)
- Template dna (66 kDa, DNA from synthetic construct)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Non-template dna (64 kDa, DNA from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from pig)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
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 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to csb, crl4csa, uvssa, paf and spt6. (Complex)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Supplementary proteins (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 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 rpb9 (14 kDa, Protein from Pig)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Nts, rna, ts (Complex from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 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 Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
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 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Complex between transcribing pol ii, tcr factors and elongation factors spt6 and paf. (Complex)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Pig)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog (133 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Supplementory proteins (Complex from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
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 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Pig)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Supplementary proteins (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 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 rpb9 (14 kDa, Protein from Pig)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Nts, rna, ts (Complex from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to trc factors, spt6 and paf. (Complex)
- 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 Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ted
Q-score: 0.338
Vos SM, Farnung L, Linden A, Urlaub H, Cramer P
Nat Struct Mol Biol (2020) 27 pp. 668-677 [ Pubmed: 32541898 DOI: doi:10.1038/s41594-020-0437-1 ]
- Transcription elongation factor spt4 and spt5 (Complex from Homo sapiens)
- Dna/rna (Complex from synthetic construct)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Uncharacterized protein (7 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Uncharacterized protein (13 kDa, Protein from Pig)
- Human transcription factors and associated proteins (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rna polymerase ii subunit c (31 kDa, Protein from Pig)
- Dna (37-mer) (14 kDa, DNA from synthetic construct)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Uncharacterized protein (7 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Complete ec* (1 MDa, Complex)
- Pig dna/rna polymerase subunits (Complex from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Pig)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*ap*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (14 kDa, RNA from synthetic construct)
- Rna polymerase ii subunit g (19 kDa, Protein from Pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Rna polymerase ii subunit d (16 kDa, Protein from Pig)
Structure of activated transcription complex Pol II-DSIF-PAF-SPT6 (Map A)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6gmh
Q-score: 0.324
Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P
Nature (2018) 560 pp. 607-612 [ DOI: doi:10.1038/s41586-018-0440-4 Pubmed: 30135578 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Rpb12 (7 kDa, Protein from Pig)
- Paf1,rna polymerase ii-associated factor 1 homolog,rna polymerase ii-associated factor 1 homolog (67 kDa, Protein from Homo sapiens)
- Rpb1 (217 kDa, Protein from Pig)
- Rpb11 (13 kDa, Protein from Pig)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rpb10 (7 kDa, Protein from Pig)
- Nucleic acids (Complex from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Associated proteins (Complex from Homo sapiens)
- Rna polymerase ii subunit c (31 kDa, Protein from Pig)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Ctr9,rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein ctr9 homolog (125 kDa, Protein from Homo sapiens)
- Leo1,leo1,rna polymerase-associated protein leo1 (84 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Rna polymerase ii-dsif-paf-spt6 elongation complex (ec*) (1 MDa, Complex)
- Transcription elongation factor spt6,transcription elongation factor spt6,transcription elongation factor spt6 (198 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Template dna (14 kDa, DNA from synthetic construct)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Rna polymerase ii subunit g (19 kDa, Protein from Pig)
- Cdc73 (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Rna polymerase ii subunit d (16 kDa, Protein from Pig)