RNA Polymerase II dimer (Class 3)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7ozp
Q-score: 0.328
Aibara S, Dienemann C, Cramer P
Nucleic Acids Res (2021) 49 pp. 10747-10755 [ Pubmed: 34530439 DOI: doi:10.1093/nar/gkab783 ]
- Rna polymerase ii dimer (1 MDa, Complex from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
Overall map of a transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7b0y
Q-score: 0.344
Zhang S, Aibara S, Vos SM, Agafonov DE, Luhrmann R, Cramer P
Science (2021) 371 pp. 305-309 [ Pubmed: 33446560 DOI: doi:10.1126/science.abf1870 ]
- The transcribing rna polymerase ii-u1 snrnp complex with 145-nt rna (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- U1 small nuclear ribonucleoprotein 70 kda (51 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- U1 snrna (52 kDa, RNA from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Nucleic acids (Complex from synthetic construct)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- U1 snrnp (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- U1 small nuclear ribonucleoprotein a (31 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein-associated protein (23 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- 145-nt rna (46 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
Structure of paused transcription complex Pol II-DSIF-NELF
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6gml
Q-score: 0.34
Vos SM, Farnung L, Urlaub H, Cramer P
Nature (2018) 560 pp. 601-606 [ Pubmed: 30135580 DOI: doi:10.1038/s41586-018-0442-2 ]
- Template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Rna polymerase ii elongation complex bound to dsif and nelf (927 kDa, Complex)
- Negative elongation factor e,negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Hiv-1 pause transcription scaffold (Complex from Human immunodeficiency virus 1)
- Uncharacterized protein (13 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Uncharacterized protein (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 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)
- Tar rna (14 kDa, RNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b,negative elongation factor b (64 kDa, Protein from Homo sapiens)
- Uncharacterized protein (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Negative elongation factor c/d (64 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit c (30 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Drb sensitivity inducing factor (dsif) (Complex from Human immunodeficiency virus 1)
- Sus scrofa rna polymerase ii (Complex from Sus scrofa)
- Rna polymerase ii subunit g (19 kDa, Protein from Sus scrofa)