RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA
Resolution: 5.6 Å
EM Method: Single-particle
Fitted PDBs: 6a5l
Q-score: 0.182
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 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 ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (Complex from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (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))
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 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))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome
Resolution: 7.0 Å
EM Method: Single-particle
Fitted PDBs: 6a5p
Q-score: 0.138
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*c)-3') (3 kDa, RNA from synthetic construct)
- Rna polymerase ii subunit (18 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex stalled at shl(-5) of the nucleosome (Complex from Komagataella phaffii)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome
Resolution: 8.7 Å
EM Method: Single-particle
Fitted PDBs: 6a5r
Q-score: 0.11
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- 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 subunit (18 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*cp*up*cp*gp*up*gp*cp*cp*up*g)-3') (3 kDa, RNA from synthetic construct)
- Rna polymerase ii elongation complex stalled at shl(-2) of the nucleosome (Complex from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome
Resolution: 6.7 Å
EM Method: Single-particle
Fitted PDBs: 6a5t
Q-score: 0.151
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- 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 subunit (18 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex stalled at shl(-5) of the nucleosome (Complex from Komagataella phaffii)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
Resolution: 7.6 Å
EM Method: Single-particle
Fitted PDBs: 6a5u
Q-score: 0.14
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a, histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 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 ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2b, histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (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))
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 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 ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna, tilt conformation (Complex from Komagataella phaffii)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6inq
Q-score: 0.149
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Yeast)
- Histone h2a, histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Yeast)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Yeast)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Yeast)
- Histone h2b, histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (198-mer) (38 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Yeast)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Yeast)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Yeast)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Yeast)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Yeast)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Yeast)
- Rna (5'-r(p*gp*up*gp*up*cp*up*up*gp*gp*gp*u)-3') (3 kDa, RNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Yeast)
- Rna polymerase ii subunit (18 kDa, Protein from Yeast)
- Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (+1 position) (Complex from Komagataella phaffii)