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 excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- 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)
- Ts (15 kDa, DNA from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Pol ii-tcr-stk19 (Complex from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- 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 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)
- Isoform 1 of inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor 1 homolog (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (133 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)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
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)
Structure of the mammalian Pol II-SPT6 complex, Struture 4 (Global map)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Transcription elongation factor spt6 (Protein from Sus scrofa)
- The pol ii-spt6 transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Template dna (DNA from synthetic construct)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Rna (RNA from synthetic construct)
- Non-template dna (DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Transcription elongation factor spt6 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna (RNA from synthetic construct)
- Elongin a (Protein from Homo sapiens)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Elongin c (Protein from Homo sapiens)
- Rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Template dna (DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Non-template dna (DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Elongin b (Protein from Homo sapiens)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
Structure of the mammalian Pol II-SPT6 complex (composite map)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8oeu
Q-score: 0.526
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- 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)
- The pol ii-spt6 transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (20 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)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 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)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
Structure of the mammalian Pol II-SPT6-Elongin complex, lacking ELOA latch (composite map 2)
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8oev
Q-score: 0.468
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- 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)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (20 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)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Elongin-a (90 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)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8oew
Q-score: 0.56
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- 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)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- The pol ii-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (20 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)
- Magnesium ion (24 Da, Ligand)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Elongin-a (90 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)
- Non-template dna (14 kDa, DNA from synthetic construct)
Structure of the mammalian Pol II-SPT6-Elongin complex, Structure 1 (local resolution filtered map)
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8of0
Q-score: 0.422
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- 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)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (20 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)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Elongin-a (90 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)
- Non-template dna (14 kDa, DNA from synthetic construct)
Structure of the Pol II-TCR-ELOF1 complex.
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8b3d
Q-score: 0.532
To Be Published
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Pol ii-tcr-elof1 complex. (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Ts (15 kDa, DNA from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna (3 kDa, RNA from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 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)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rpb7 (28 kDa, Protein from Sus scrofa domesticus)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8b3f
Q-score: 0.456
To Be Published
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Ts (15 kDa, DNA from Homo sapiens)
- Pol ii-csb-csa-ddb1-elof1 complex. (Complex from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Rna (3 kDa, RNA from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- 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 domesticus)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 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)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)