Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7wbv
Q-score: 0.267
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ DOI: doi:10.1016/j.jmb.2023.168130 Pubmed: 37120012 ]
- Transcription elongation factor spt5 (91 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- 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)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-4) of the nucleosome (Complex from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*up*gp*gp*cp*cp*gp*up*up*up*up*cp*gp*up*up*gp*u)-3') (5 kDa, RNA from synthetic construct)
- Dna (159-mer) (60 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5 (Complex from Homo sapiens)
- Dna, rna (Complex)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Resolution: 7.1 Å
EM Method: Single-particle
Fitted PDBs: 7wbw
Q-score: 0.137
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ DOI: doi:10.1016/j.jmb.2023.168130 Pubmed: 37120012 ]
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- 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)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*up*up*up*up*cp*gp*up*up*gp*up*up*up*up*up*u)-3') (4 kDa, RNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-3.5) of the nucleosome (Complex from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5 (Complex from Homo sapiens)
- Dna, rna (Complex)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7wbx
Q-score: 0.298
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ DOI: doi:10.1016/j.jmb.2023.168130 Pubmed: 37120012 ]
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-3) of the nucleosome (Complex from Komagataella pastoris)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5 (Complex from Homo sapiens)
- Dna, rna (Complex)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*up*cp*gp*up*up*gp*up*up*up*up*up*up*up*cp*up*g)-3') (4 kDa, RNA from synthetic construct)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Resolution: 6.95 Å
EM Method: Single-particle
Fitted PDBs: 8he5
Q-score: 0.105
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ Pubmed: 37120012 DOI: doi:10.1016/j.jmb.2023.168130 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rad26 (Complex from Komagataella phaffii)
- Histone (Complex from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii elongation complex (Complex from Homo sapiens)
- Transcription elongation factor elf1 (Complex)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna repair protein (125 kDa, Protein from Komagataella phaffii)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 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)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*up*up*up*up*cp*gp*up*up*gp*up*up*up*up*up*u)-3') (4 kDa, RNA from synthetic construct)
- Dna, rna (Complex from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with rad26 and elf1, stalled at shl(-3.5) of the nucleosome (Complex from Komagataella phaffii)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)