Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9j0n
Q-score: 0.316
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Non-template dna (157-mer) (61 kDa, DNA from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Template dna (168-mer) (60 kDa, DNA from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*cp*c)-3') (13 kDa, RNA from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0o
Q-score: 0.313
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0p
Q-score: 0.311
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8yfq
Q-score: 0.393
Yanagisawa T, Murayama Y, Ehara H, Goto M, Aoki M, Sekine SI
Nat Commun (2024) 15 pp. 7854-7854 [ Pubmed: 39245712 DOI: doi:10.1038/s41467-024-52157-0 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna (90-mer) (27 kDa, DNA from synthetic construct)
- Decapping nuclease (44 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Rna (22-mer) (7 kDa, RNA from synthetic construct)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Cryo em structure of komagataella phaffii rnapii-rat1-rai1 pre-termination complex (Complex from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- 5'-3' exoribonuclease (115 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (90-mer) (27 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8yfr
Q-score: 0.366
Yanagisawa T, Murayama Y, Ehara H, Goto M, Aoki M, Sekine SI
Nat Commun (2024) 15 pp. 7854-7854 [ Pubmed: 39245712 DOI: doi:10.1038/s41467-024-52157-0 ]
- Komagataella phaffii rat1-rai1 complex bound within the rnapii cleft (Complex from Komagataella phaffii)
- Decapping nuclease (44 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- 5'-3' exoribonuclease (115 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)