Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 8jh2
Q-score: 0.145
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ Pubmed: 37981206 DOI: doi:10.1016/j.jbc.2023.105477 ]
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Histones (Complex from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc27 (24 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna (Complex)
- Rna (5'-r(p*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*g)-3') (5 kDa, RNA from synthetic construct)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Homo sapiens)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8jh3
Q-score: 0.255
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ Pubmed: 37981206 DOI: doi:10.1016/j.jbc.2023.105477 ]
- Rna (Complex)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Histones (Complex from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- 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)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*gp)-3') (4 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8jh4
Q-score: 0.313
Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H
J Biol Chem (2023) 299 pp. 105477-105477 [ Pubmed: 37981206 DOI: doi:10.1016/j.jbc.2023.105477 ]
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Histones (Complex from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna (Complex)
- Rna (5'-r(p*gp*up*cp*up*up*gp*gp*gp*up*gp)-3') (3 kDa, RNA from synthetic construct)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii (Complex from Homo sapiens)
Cryo-EM structure of the human nucleosome containing H3.8
Resolution: 2.26133 Å
EM Method: Single-particle
Fitted PDBs: 8kb5
Q-score: 0.655
Hirai S, Kujirai T, Akatsu M, Ogasawara M, Ehara H, Sekine SI, Ohkawa Y, Takizawa Y, Kurumizaka H
J.Biochem. (2023) 174 pp. 549-559 [ DOI: doi:10.1093/jb/mvad069 Pubmed: 37757444 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- The human nucleosome containing h3.8 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.8 (16 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human nucleosome with scFv
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8jl9
Q-score: 0.569
Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H
Nucleic Acids Res (2023) 51 pp. 10364-10374 [ Pubmed: 37718728 DOI: doi:10.1093/nar/gkad754 ]
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- The 193 bp human nucleosome with scfv (Complex from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8jla
Q-score: 0.453
Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H
Nucleic Acids Res (2023) 51 pp. 10364-10374 [ Pubmed: 37718728 DOI: doi:10.1093/nar/gkad754 ]
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h4 (10 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Histone h3.1 (12 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (11 kDa, Protein from Homo sapiens)
- The human nucleosome lacking n-terminal region of h2a, h2b, h3, and h4 with scfv (Complex from Homo sapiens)
Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant
Resolution: 2.36 Å
EM Method: Single-particle
Fitted PDBs: 8jlb
Q-score: 0.602
Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H
Nucleic Acids Res (2023) 51 pp. 10364-10374 [ Pubmed: 37718728 DOI: doi:10.1093/nar/gkad754 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- The 145 bp human nucleosome containing h3.2 c110a mutant with scfv (Complex from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8jld
Q-score: 0.579
Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H
Nucleic Acids Res (2023) 51 pp. 10364-10374 [ Pubmed: 37718728 DOI: doi:10.1093/nar/gkad754 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- The 145 bp human nucleosome containing acetylated h3 tail with scfv (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)