Ternary complex of RNA Pol II, transcription scaffold and Rad26
Resolution: 5.8 Å
EM Method: Single-particle
Fitted PDBs: 5vvr
Q-score: 0.174
Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D
Nature (2017) 551 pp. 653-657 [ DOI: doi:10.1038/nature24658 Pubmed: 29168508 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (nts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Dna (ts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Ternary complex of rna pol ii, transcription scaffold and rad26 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna (3 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair and recombination protein rad26 (124 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 6.4 Å
EM Method: Single-particle
Fitted PDBs: 5vvs
Q-score: 0.184
Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D
Nature (2017) 551 pp. 653-657 [ DOI: doi:10.1038/nature24658 Pubmed: 29168508 ]
- Binary complex of rna pol ii and transcription scaffold (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna (3 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (nts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (ts) (14 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of an RNA polymerase II-DSIF transcription elongation complex
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol (2017) 24 pp. 809-815 [ DOI: doi:10.1038/nsmb.3465 Pubmed: 28892040 ]
- Dsif (130 kDa, Complex from Homo sapiens)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC2
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol (2017) 24 pp. 809-815 [ Pubmed: 28892040 DOI: doi:10.1038/nsmb.3465 ]
- Dsif (130 kDa, Complex from Homo sapiens)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
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 [ Pubmed: 28892040 DOI: doi:10.1038/nsmb.3465 ]
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Bos taurus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Bos taurus)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Bos taurus)
- Polymerase (rna) ii (dna directed) polypeptide d (16 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Bos taurus)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- 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)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Bos taurus)
- Uncharacterized protein (17 kDa, Protein from Bos taurus)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
- Dsif (130 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Bos taurus)
Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC4
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol (2017) 24 pp. 809-815 [ DOI: doi:10.1038/nsmb.3465 Pubmed: 28892040 ]
- Dsif (130 kDa, Complex from Homo sapiens)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC5
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol (2017) 24 pp. 809-815 [ Pubmed: 28892040 DOI: doi:10.1038/nsmb.3465 ]
- Dsif (130 kDa, Complex from Homo sapiens)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS
Resolution: 3.83 Å
EM Method: Single-particle
Fitted PDBs: 5xon
Q-score: 0.336
Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI
Science (2017) 357 pp. 921-924 [ DOI: doi:10.1126/science.aan8552 Pubmed: 28775211 ]
- Spt4/5 and tfiis (Complex)
- Rna polymerase ii (Complex)
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- General transcription elongation factor tfiis (21 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc14.5, common to rna polymerases i, ii, and iii (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (30-mer) (9 kDa, RNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex bound with spt4/5 and tfiis (Complex from Komagataella pastoris)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (48-mer) (14 kDa, DNA from synthetic construct)
- Protein that forms a complex with spt4p (68 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit, found in rna polymerase complexes i, ii, and iii (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Xu Y, Bernecky C, Lee CT, Maier KC, Schwalb B, Tegunov D, Plitzko JM, Urlaub H, Cramer P
Nat Commun (2017) 8 pp. 15741-15741 [ Pubmed: 28585565 DOI: doi:10.1038/ncomms15741 ]
- Paf1c (340 kDa, Complex from Saccharomyces cerevisiae S288c)
- Rna polymerase ii-paf1c-tfiis (900 kDa, Complex)
- Tfiis (35 kDa, Complex from Saccharomyces cerevisiae)
- Rna polymerase ii (500 kDa, Complex from Saccharomyces cerevisiae)
RNA polymerase II-Paf1C-TFIIS-A
Xu Y, Bernecky C, Lee CT, Maier KC, Schwalb B, Tegunov D, Plitzko JM, Urlaub H, Cramer P
Nat Commun (2017) 8 pp. 15741-15741 [ Pubmed: 28585565 DOI: doi:10.1038/ncomms15741 ]
- Rna polymerase ii-paf1c-tfiis-a (900 kDa, Complex)
- Paf1c (340 kDa, Complex from Saccharomyces cerevisiae)
- Tfiis (35 kDa, Complex from Saccharomyces cerevisiae)
- Rna polymerase ii (500 kDa, Complex from Saccharomyces cerevisiae)