Do data resources managed by EMBL-EBI and our collaborators make a difference to your work? Please take 10 minutes to fill in our annual user survey, and help us make the case for why sustaining open data resources is critical for life sciences research. We appreciate your responses prior to closing of the survey on Monday 17th June.
Cryo-EM structure of human topoisomerase II beta in complex with DNA and etoposide
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7yq8
Q-score: 0.396
Bunch H, Kim D, Naganuma M, Nakagawa R, Cong A, Jeong J, Ehara H, Vu H, Chang JH, Schellenberg MJ, Sekine SI
Nat Commun (2023) 14 pp. 8341-8341 [ Pubmed: 38097570 DOI: doi:10.1038/s41467-023-44089-y ]
- Dna topoisomerase 2-beta (183 kDa, Protein from Homo sapiens)
- (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-o-[(1r)-ethylidene]-beta-d-glucopyranoside (588 Da, Ligand)
- Human topoisomerase ii beta (Complex from Homo sapiens)
- 50-mer dna (15 kDa, DNA from Homo sapiens)
- 50-mer dna (15 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Ternary complex of human topoisomerase ii beta with dna and etoposide (Complex)
- Dna (Complex)
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 ]
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- 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 (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)
- Rna polymerase ii (Complex from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Transcription elongation factor spt4 (12 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 (Complex)
- Rna polymerase subunit abc27 (24 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (40-mer) (12 kDa, DNA 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 b32 (20 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)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
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 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- 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)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii (Complex from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*gp)-3') (4 kDa, RNA from synthetic construct)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- 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 subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 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)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- 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 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- 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)
- Rna (5'-r(p*gp*up*cp*up*up*gp*gp*gp*up*gp)-3') (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii (Complex from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- 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 subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 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)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
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 ]
- Histones (Complex from Homo sapiens)
- Rna polymerase ii (Complex from Komagataella phaffii)
- Dna, rna (Complex from synthetic construct)
- Rna polymerase ii - nucleosome complex (Complex)
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 ]
- The human nucleosome containing h3.8 (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 h3.8 (16 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
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 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 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)
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 ]
- Histone h2b type 1-j (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h3.1 (12 kDa, Protein from Homo sapiens)
- The human nucleosome lacking n-terminal region of h2a, h2b, h3, and h4 with scfv (Complex from Homo sapiens)
- Histone h4 (10 kDa, Protein 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 h3.2 (15 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)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- 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)
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)
- 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 h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)