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 [ DOI: doi:10.1016/j.jbc.2023.105477 Pubmed: 37981206 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- Transcription elongation factor 1 homolog (12 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 (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc27 (24 kDa, Protein from Komagataella phaffii)
- 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 ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Dna (218-mer) (70 kDa, DNA from synthetic construct)
- 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)
- Rna polymerase ii (Complex from Homo sapiens)
- 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)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
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 [ DOI: doi:10.1016/j.jbc.2023.105477 Pubmed: 37981206 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 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 ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- 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)
- Rna polymerase ii (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
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 [ DOI: doi:10.1016/j.jbc.2023.105477 Pubmed: 37981206 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii - nucleosome complex (Complex from Komagataella phaffii)
- Rna (5'-r(p*gp*up*cp*up*up*gp*gp*gp*up*gp)-3') (3 kDa, RNA from synthetic construct)
- 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)
- Rna polymerase ii (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histones (Complex from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna (Complex from synthetic construct)
Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8grm
Q-score: 0.516
Ai HS, Tong Z, Deng Z, Tian J, Zhang L, Sun M, Du Y, Xu Z, Shi Q, Liang L, Zheng Q, Li JB, Pan M, Liu L
Chem (2023) [ DOI: doi:10.1016/j.chempr.2023.01.012 ]
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Complex of prc1 and h2ak119-ubch5b-ub nucleosome (350 kDa, Complex from Homo sapiens)
- Ring1b (11 kDa, Protein from Homo sapiens)
- Commd3 protein (11 kDa, Protein from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Ubch5b (16 kDa, Protein from Homo sapiens)
Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome
Resolution: 3.87 Å
EM Method: Single-particle
Fitted PDBs: 8grq
Q-score: 0.352
Ai HS, Tong Z, Deng Z, Tian J, Zhang L, Sun M, Du Y, Xu Z, Shi Q, Liang L, Zheng Q, Li JB, Pan M, Liu L
Chem (2023) [ DOI: doi:10.1016/j.chempr.2023.01.012 ]
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2d 3 (ubc4/5 homolog, yeast), isoform cra_a (16 kDa, Protein from Homo sapiens)
- Complex of brca1/bard1 and h2ak127-ubch5c-ub nucleosome (Complex from Homo sapiens)
- H2b (20 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-h (12 kDa, Protein from Homo sapiens)
- Breast cancer type 1 susceptibility protein (10 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Brca1-associated ring domain protein 1 (10 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
SIRT6 bound to an H3K9Ac nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8f86
Q-score: 0.434
Wang ZA, Markert JW, Whedon SD, Yapa Abeywardana M, Lee K, Jiang H, Suarez C, Lin H, Farnung L, Cole PA
J Am Chem Soc (2023) 145 pp. 6811-6822 [ DOI: doi:10.1021/jacs.2c13512 Pubmed: 36930461 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- [(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3ar,5r,6r,6ar)-6-hydroxytetrahydro-2h-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) (587 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Sirt6 bound to h3k9ac (Complex)
- Dna (148-mer) (56 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Nad-dependent protein deacylase sirtuin-6 (39 kDa, Protein from Homo sapiens)
- Dna (148-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 7xcr
Q-score: 0.571
Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L
Nat Chem Biol (2022) 18 pp. 972-980 [ Pubmed: 35739357 DOI: doi:10.1038/s41589-022-01067-7 ]
- Histone h4 (10 kDa, Protein from Homo sapiens)
- Histone h2a (11 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (37 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Complex of dot1l(1-416) and h2bk34ub nucleosome (Complex from Homo sapiens)
- Dna (146-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Histone domain-containing protein (11 kDa, Protein from synthetic construct)
Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 7xct
Q-score: 0.514
Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L
Nat Chem Biol (2022) 18 pp. 972-980 [ Pubmed: 35739357 DOI: doi:10.1038/s41589-022-01067-7 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a (11 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (37 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Complex of dot1l(1-416) and h2bk34ub 2:1 nucleosome (Complex from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone domain-containing protein (11 kDa, Protein from Homo sapiens)
- Histone h4 (10 kDa, Protein from Homo sapiens)
cryo-EM structure of H2BK34ub nucleosome
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 7xd0
Q-score: 0.457
Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L
Nat Chem Biol (2022) 18 pp. 972-980 [ Pubmed: 35739357 DOI: doi:10.1038/s41589-022-01067-7 ]
- Ubiquitin-60s ribosomal protein l40 (8 kDa, Protein from synthetic construct)
- Histone h2a (11 kDa, Protein from Homo sapiens)
- Histone domain-containing protein (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from synthetic construct)
- H2bk34ub nucleosome (Complex from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (146-mer) (44 kDa, DNA from synthetic construct)
cryo-EM structure of unmodified nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xd1
Q-score: 0.558
Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L
Nat Chem Biol (2022) 18 pp. 972-980 [ Pubmed: 35739357 DOI: doi:10.1038/s41589-022-01067-7 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Unmodified nucleosome (Complex from Homo sapiens)