Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9j0n
Q-score: 0.316
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- 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)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Template dna (168-mer) (60 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Non-template dna (157-mer) (61 kDa, DNA from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*cp*c)-3') (13 kDa, RNA from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0o
Q-score: 0.313
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- 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)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0p
Q-score: 0.311
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- 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)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
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)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egx
Q-score: 0.25
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Rna (6 kDa, RNA from synthetic construct)
- 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)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- 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)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Setd2 downstream complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Non-template dna (63 kDa, DNA from synthetic construct)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egy
Q-score: 0.256
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Rna (6 kDa, RNA from synthetic construct)
- 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)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- 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)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Setd2 downstream complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Non-template dna (63 kDa, DNA from synthetic construct)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egz
Q-score: 0.261
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Rna (6 kDa, RNA from synthetic construct)
- 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)
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- 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)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Setd2 downstream complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Non-template dna (63 kDa, DNA from synthetic construct)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 9eh0
Q-score: 0.24
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Non-template (60 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna (4 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- 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)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- 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)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Template dna (61 kDa, DNA from synthetic construct)
- Setd2 downstream complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9eh2
Q-score: 0.252
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Fact complex subunit spt16 (120 kDa, Protein from Homo sapiens)
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Fact complex subunit ssrp1 (81 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- 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)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- 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)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Setd2 downstream complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Template dna (66 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna (3 kDa, RNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8a3y
Q-score: 0.231
Farnung L, Ochmann M, Garg G, Vos SM, Cramer P
Mol Cell (2022) 82 pp. 3126-3134.e7 [ Pubmed: 35858621 DOI: doi:10.1016/j.molcel.2022.06.027 ]
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna, template dna (9 kDa, RNA from synthetic construct)
- Non-template dna (39 kDa, DNA from synthetic construct)
- Rna polymerase ii-associated factor 1 homolog (36 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Spt6 (117 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- 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 polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna, template dna (42 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Mammalian pol ii-tfiis elongation complex (Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein leo1 (210 kDa, Protein from Homo sapiens)