Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qzm
Q-score: 0.506
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
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 [ Pubmed: 39196936 DOI: doi:10.1126/sciadv.adp0975 ]
- Dna (cytosine-5)-methyltransferase 3a (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Dnmt3a1 udr in complex with h2ak119ub-nucleosome (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8u5h
Q-score: 0.443
Chen X, Guo Y, Zhao T, Lu J, Fang J, Wang Y, Wang GG, Song J
Nat Commun (2024) 15 pp. 6217-6217 [ DOI: doi:10.1038/s41467-024-50526-3 Pubmed: 39043678 ]
- Dna (cytosine-5)-methyltransferase 3a (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Dnmt3a n-terminal domain and h2ak119ub nucleosome complex (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Xenopus laevis)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 6pa7
Q-score: 0.403
Xu TH, Liu M, Zhou XE, Liang G, Zhao G, Xu HE, Melcher K, Jones PA
Nature (2020) 586 pp. 151-155 [ Pubmed: 32968275 DOI: doi:10.1038/s41586-020-2747-1 ]
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase (Complex from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- Dna (167-mer) (Complex from synthetic construct)
- Dna (cytosine-5)-methyltransferase 3a (77 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- A ternary complex of dnmt3a/b asymmetrically binds to the nucleosomes (520 kDa, Complex)
- Dna (cytosine-5)-methyltransferase 3b (86 kDa, Protein from Homo sapiens)