Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome
Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C
Sci Adv (2024) 10 pp. eadp0975-eadp0975 [ DOI: doi:10.1126/sciadv.adp0975 Pubmed: 39196936 ]
- Dna (146-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dnmt3a1 udr in complex with h2ak119ub-nucleosome (Complex from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase 3a (9 kDa, Protein from Homo sapiens)
Human canonical 601 DNA nucleosome
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8jbx
Q-score: 0.43
Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T
Nucleic Acids Res (2024) 52 pp. 11612-11625 [ Pubmed: 39329259 DOI: doi:10.1093/nar/gkae825 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Human canonical histone (Complex from Homo sapiens)
- Human canonical histone and 601 dna (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 dna (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 8jcc
Q-score: 0.398
Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T
Nucleic Acids Res (2024) 52 pp. 11612-11625 [ Pubmed: 39329259 DOI: doi:10.1093/nar/gkae825 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type w-t (16 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- H2bfwt nucleosome (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Human H2BFWTH100R nucleosome with 601 DNA
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8jcd
Q-score: 0.445
Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T
Nucleic Acids Res (2024) 52 pp. 11612-11625 [ Pubmed: 39329259 DOI: doi:10.1093/nar/gkae825 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type w-t (16 kDa, Protein from Homo sapiens)
- Human canonical histone (Complex from Homo sapiens)
- Human canonical histone and 601 dna (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 dna (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Eaf3 CHD domain bound to the nucleosome
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8ihm
Q-score: 0.434
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ Pubmed: 37845487 DOI: doi:10.1038/s41422-023-00884-2 ]
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Rco1-abr (2 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (13 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of the Rpd3S core complex
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8ihn
Q-score: 0.48
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ Pubmed: 37845487 DOI: doi:10.1038/s41422-023-00884-2 ]
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (2 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 8iht
Q-score: 0.345
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ Pubmed: 37845487 DOI: doi:10.1038/s41422-023-00884-2 ]
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Structure of nucleosome-bound SRCAP-C in the apo state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x15
Q-score: 0.218
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ Pubmed: 38331872 DOI: doi:10.1038/s41421-023-00640-1 ]
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (137-mer) (42 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the apo state (Complex from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Dna (137-mer) (41 kDa, DNA from synthetic construct)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1, n-terminally processed (41 kDa, Protein from Homo sapiens)
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x19
Q-score: 0.292
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ Pubmed: 38331872 DOI: doi:10.1038/s41421-023-00640-1 ]
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the adp-befx-bound state (Complex from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
Structure of nucleosome-bound SRCAP-C in the ADP-bound state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x1c
Q-score: 0.297
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ Pubmed: 38331872 DOI: doi:10.1038/s41421-023-00640-1 ]
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the adp-bound state (Complex from Homo sapiens)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)