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 ]
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 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 [ 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)
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 [ Pubmed: 39043678 DOI: doi:10.1038/s41467-024-50526-3 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase 3a (11 kDa, Protein from Homo sapiens)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dnmt3a n-terminal domain and h2ak119ub nucleosome complex (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
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 [ DOI: doi:10.1038/s41586-020-2747-1 Pubmed: 32968275 ]
- Dna (cytosine-5)-methyltransferase 3a (77 kDa, Protein from Homo sapiens)
- A ternary complex of dnmt3a/b asymmetrically binds to the nucleosomes (520 kDa, Complex)
- Histone (Complex from Xenopus laevis)
- Dna (167-mer) (Complex from synthetic construct)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase 3b (86 kDa, Protein from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- Dna (cytosine-5)-methyltransferase (Complex from Homo sapiens)