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 ]
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Bos taurus)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Bos taurus)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Bos taurus)
- Uncharacterized protein (17 kDa, Protein from Bos taurus)
- Polymerase (rna) ii (dna directed) polypeptide d (16 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA 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)
- Zinc ion (65 Da, Ligand)
- Dsif (130 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Bos taurus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Bos taurus)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
Transcription initiation complex structures elucidate DNA opening (OC1)
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Yeast pol ii transcription initiation complex (open dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (open) (44 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation complex structures elucidate DNA opening (OC2-focused)
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Yeast pol ii transcription initiation complex (open dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (open) (44 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation complex structures elucidate DNA opening (OC3)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 5fyw
Q-score: 0.26
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Yeast pol ii transcription initiation complex (open dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (open) (44 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation complex structures elucidate DNA opening (OC3-focused)
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Yeast pol ii transcription initiation complex (open dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (open) (44 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation complex structures elucidate DNA opening (OC4)
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Yeast pol ii transcription initiation complex (open dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (open) (44 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation complex structures elucidate DNA opening (OC4-focused)
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Yeast pol ii transcription initiation complex (open dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (open) (44 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation complex structures elucidate DNA opening (OC5)
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Yeast pol ii transcription initiation complex (open dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (44 kDa, DNA from unidentified)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Transcription initiation complex structures elucidate DNA opening (CC)
Resolution: 8.8 Å
EM Method: Single-particle
Fitted PDBs: 5fz5
Q-score: 0.113
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature (2016) 533 pp. 353-358 [ DOI: doi:10.1038/NATURE17990 Pubmed: 27193681 ]
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iif (129 kDa, Protein from Saccharomyces cerevisiae)
- Synthetic promoter dna construct (closed) (DNA from unidentified)
- Yeast pol ii transcription initiation complex (closed dna) (890 kDa, Sample)
- Transcription factor iie (91 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii (513 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription factor iia (45 kDa, Protein from Saccharomyces cerevisiae)
Structure of transcribing mammalian RNA polymerase II (EC2)
Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P
Nature (2016) 529 pp. 551-554 [ DOI: doi:10.1038/nature16482 Pubmed: 26789250 ]
- Dna-directed rna polymerase ii subunit grinl1a (40 kDa, Protein from Homo sapiens)
- Dna-rna synthetic construct (30 kDa, Macromolecule from unidentified)
- Bovine pol ii elongation complex (590 kDa, Sample)
- Dna-directed rna polymerase ii (520 kDa, Protein from Bos taurus)