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 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii dimer (1 MDa, Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 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 [ DOI: doi:10.1126/science.abf1870 Pubmed: 33446560 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Rpb12 (7 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Small nuclear ribonucleoprotein g (8 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 d3 (13 kDa, Protein from Homo sapiens)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- U1 snrna (52 kDa, RNA from Homo sapiens)
- 145-nt rna (46 kDa, RNA from synthetic construct)
- Small nuclear ribonucleoprotein-associated protein (23 kDa, Protein from Homo sapiens)
- Nucleic acids (Complex from synthetic construct)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- The transcribing rna polymerase ii-u1 snrnp complex with 145-nt rna (Complex)
- U1 small nuclear ribonucleoprotein a (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- U1 snrnp (Complex from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- U1 small nuclear ribonucleoprotein 70 kda (51 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa domesticus)
Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC3
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5oik
Q-score: 0.373
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol (2017) 24 pp. 809-815 [ DOI: doi:10.1038/nsmb.3465 Pubmed: 28892040 ]
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Bos taurus)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*ap*up*ap*up*ap*cp*ap*up*ap*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3') (16 kDa, RNA from synthetic construct)
- Uncharacterized protein (17 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
- Dsif (130 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Bos taurus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Bos taurus)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Bos taurus)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Bos taurus)
- Polymerase (rna) ii (dna directed) polypeptide d (16 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Bos taurus)