Structure of paused transcription complex Pol II-DSIF-NELF - tilted
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8uha
Q-score: 0.28
Mol Cell (2024) 84 pp. 1243- [ Pubmed: 38401543 DOI: doi:10.1016/j.molcel.2024.01.023 ]
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 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 polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna (28-mer) (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna (5 kDa, RNA from synthetic construct)
- Dna (38-mer) (15 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase in complex with dsif and nelf (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structure of paused transcription complex Pol II-DSIF-NELF - post-translocated
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8uhd
Q-score: 0.353
Mol Cell (2024) 84 pp. 1243- [ Pubmed: 38401543 DOI: doi:10.1016/j.molcel.2024.01.023 ]
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (30 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 polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Template dna (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase in complex with dsif and nelf (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
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- [ Pubmed: 38401543 DOI: doi:10.1016/j.molcel.2024.01.023 ]
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 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 polymerase subunit (217 kDa, Protein from Sus scrofa)
- Rna polymerase in complex with dsif and nelf (Complex from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (15 kDa, DNA from synthetic construct)
- Template dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna (5 kDa, RNA from synthetic construct)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Negative elongation factor b (63 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
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- [ Pubmed: 38401543 DOI: doi:10.1016/j.molcel.2024.01.023 ]
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 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 polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Rna polymerase in complex with dsif and nelf (Complex from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna (5 kDa, RNA from synthetic construct)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Negative elongation factor b (63 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structure of transcription complex Pol II-DSIF-NELF-TFIIS
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8uis
Q-score: 0.319
Mol Cell (2024) 84 pp. 1243- [ Pubmed: 38401543 DOI: doi:10.1016/j.molcel.2024.01.023 ]
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (15 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase in complex with dsif, nelf, tfiis (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structure of Pol II-DSIF-NELF - post-translocated
Mol Cell (2024) 84 pp. 1243-1256.e5 [ Pubmed: 38401543 DOI: doi:10.1016/j.molcel.2024.01.023 ]
- Rpb9 (Protein from Sus scrofa)
- Nelf-c (Protein from Homo sapiens)
- Rpb2 (Protein from Sus scrofa)
- Rpb10 (Protein from Sus scrofa)
- Rpb11 (Protein from Sus scrofa)
- Rpb4 (Protein from Sus scrofa)
- Spt4 (Protein from Homo sapiens)
- Rpb12 (Protein from Sus scrofa)
- Template dna (DNA from synthetic construct)
- Rpb7 (Protein from Sus scrofa)
- Rpb6 (Protein from Sus scrofa)
- Non-template dna (DNA from synthetic construct)
- Rpb1 (Protein from Sus scrofa)
- Nelf-e (Protein from Homo sapiens)
- Nelf-a (Protein from Homo sapiens)
- Rna (RNA from synthetic construct)
- Spt5 (Protein from Homo sapiens)
- Rna polymerase in complex with dsif and nelf (Complex)
- Rpb8 (Protein from Sus scrofa)
- Rpb3 (Protein from Sus scrofa)
- Rpb5 (Protein from Sus scrofa)
- Nelf-b (Protein from Homo sapiens)