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 (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Dna (cytosine-5)-methyltransferase 3a (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dnmt3a1 udr in complex with h2ak119ub-nucleosome (Complex 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')
H2BK120ub-modified nucleosome ubiquitin position 1
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8v25
Q-score: 0.519
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ Pubmed: 39149911 DOI: doi:10.1093/nar/gkae698 ]
- H2bk120ub-modified nucleosome (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histones (Complex from Xenopus laevis)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H2BK120ub-modified nucleosome ubiquitin position 2
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8v26
Q-score: 0.515
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histones (Complex from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- H2bk120ub-modified nucleosome (Complex)
- Ubiquitin (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
H2BK120ub-modified nucleosome ubiquitin position 3
Resolution: 3.34 Å
EM Method: Single-particle
Fitted PDBs: 8v27
Q-score: 0.516
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histones (Complex from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- H2bk120ub-modified nucleosome (Complex)
- Ubiquitin (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
H2BK120ub-modified nucleosome ubiquitin position 4
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 8v28
Q-score: 0.505
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histones (Complex from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- H2bk120ub-modified nucleosome (Complex)
- Ubiquitin (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8g6g
Q-score: 0.575
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H2bk120ub+h3k79me2-modified nucleosome (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8g6h
Q-score: 0.552
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H2bk120ub+h3k79me2-modified nucleosome (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
H2AK119ub-modified nucleosome ubiquitin position 1
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8g6q
Q-score: 0.434
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ DOI: doi:10.1093/nar/gkae698 Pubmed: 39149911 ]
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H2ak119ub-modified nucleosome (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
H2AK119ub-modified nucleosome ubiquitin position 2
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8g6s
Q-score: 0.445
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C
Nucleic Acids Res (2024) 52 pp. 9978-9995 [ Pubmed: 39149911 DOI: doi:10.1093/nar/gkae698 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- H2ak119ub-modified nucleosome (Complex from Xenopus laevis)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8svf
Q-score: 0.383
Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ
Sci Adv (2023) 9 pp. eadg9832-eadg9832 [ Pubmed: 37556531 DOI: doi:10.1126/sciadv.adg9832 ]
- Dna/rna (187-mer) (58 kDa, Macromolecule from synthetic construct)
- Ubiquitin carboxyl-terminal hydrolase bap1 (80 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna/rna (327-mer) (102 kDa, Macromolecule from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Bap1/asxl1 bound to the h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Polycomb group protein asxl1 (165 kDa, Protein from Homo sapiens)