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 ]
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- 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)
- Rna, template dna (42 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (36 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Non-template dna (39 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna, template dna (9 kDa, RNA from synthetic construct)
- 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 ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- 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)
- Spt6 (117 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
Structure of paused transcription complex Pol II-DSIF-NELF - poised post-translocated
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8uhg
Q-score: 0.353
Mol Cell (2024) 84 pp. 1243- [ DOI: doi:10.1016/j.molcel.2024.01.023 Pubmed: 38401543 ]
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Negative elongation factor b (63 kDa, Protein from Homo sapiens)
- Template dna (11 kDa, DNA from synthetic construct)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (19 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 rpabc2 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase in complex with dsif and nelf (Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna (5 kDa, RNA from synthetic construct)
- 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)
- Non-template dna (15 kDa, DNA from synthetic construct)
Structure of poised transcription complex Pol II-DSIF-NELF - pre-translocated
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8ui0
Q-score: 0.352
Mol Cell (2024) 84 pp. 1243- [ DOI: doi:10.1016/j.molcel.2024.01.023 Pubmed: 38401543 ]
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Negative elongation factor b (63 kDa, Protein from Homo sapiens)
- Dna (15 kDa, DNA from synthetic construct)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase in complex with dsif and nelf (Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Negative elongation factor a (55 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)
- Rna (5 kDa, RNA from synthetic construct)
- 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)
Structure of mammalian Pol II-TFIIS elongation complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8a40
Q-score: 0.486
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 polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Template dna (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna (4 kDa, RNA from synthetic construct)
- 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 ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (218 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 rpb9 (14 kDa, Protein from Sus scrofa)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ Pubmed: 34265249 DOI: doi:10.1016/j.molcel.2021.06.019 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor (Complex from Homo sapiens)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Dna and rna (Complex from HIV whole-genome vector AA1305#18)
- Elongation and assocation factor (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase subunit beta (Protein from Sus scrofa)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ Pubmed: 34265249 DOI: doi:10.1016/j.molcel.2021.06.019 ]
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from pig)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from pig)
- Rna polymerase ii subunit e (Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from pig)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from pig)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from pig)
- Elongation and association factor (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (Protein from pig)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from pig)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
- Rna polymerase ii subunit d (Protein from pig)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Dna and rna (Complex from HIV whole-genome vector AA1305#18)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Rna polymerase (Complex from Sus scrofa)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Rna polymerase ii subunit k (Protein from pig)
- Rna polymerase ii subunit f (Protein from pig)
- Rna polymerase ii subunit g (Protein from pig)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Transcription elongation factor (Complex from Homo sapiens)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ Pubmed: 34265249 DOI: doi:10.1016/j.molcel.2021.06.019 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (Complex from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit beta (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Elongation factors (Complex from Homo sapiens)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ Pubmed: 34265249 DOI: doi:10.1016/j.molcel.2021.06.019 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (Complex from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase subunit beta (Protein from Sus scrofa)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Elongation factors (Complex from Homo sapiens)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Pig rna polymerase ii subunit k (Protein from Sus scrofa)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ Pubmed: 34265249 DOI: doi:10.1016/j.molcel.2021.06.019 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (Complex from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Elongation factors (Complex from Homo sapiens)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ Pubmed: 34265249 DOI: doi:10.1016/j.molcel.2021.06.019 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (Complex from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Elongation factors (Complex from Homo sapiens)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)