Histone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.

Cho CC, Huang HH, Jiang BC, Yang WZ, Chen YN, Yuan HS
Sci Adv 11(13):eadu8116 (2025 Mar 28)

PMID: 40138405 doi: 10.1126/sciadv.adu8116

Submitted to SASBDB: 2024 Nov 9 Published in SASBDB: 2025 Jan 25

SASDVZ8 – Pro-Trp-Trp-Pro (PWWP) domain from human DNA (cytosine-5)-methyltransferase 3B (DNMT3B) Sample: DNA (cytosine-5)-methyltransferase 3B Pro-Trp-Trp-Pro (PWWP) domain monomer, 17 kDa Homo sapiens protein Buffer: 20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol, pH: 8 Experiment: SAXS data collected at 13A, Taiwan Photon Source, NSRRC on 2024 Apr 20 RgGuinier 1.8 nm Dmax 6.4 nm VolumePorod 20464 nm3

SASDVK9 – Pro-Trp-Trp-Pro (PWWP) domain from human DNA (cytosine-5)-methyltransferase 3B (DNMT3B) in complex with histone H3 Sample: Histone H3.3 monomer, 4 kDa Homo sa protein DNA (cytosine-5)-methyltransferase 3B Pro-Trp-Trp-Pro (PWWP) domain monomer, 17 kDa Homo sapiens protein Buffer: 20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol, pH: 8 Experiment: SAXS data collected at 13A, Taiwan Photon Source, NSRRC on 2024 Sep 17 RgGuinier 1.8 nm Dmax 7.4 nm VolumePorod 19 nm3

SASDVL9 – Human DNA methyltransferase 3 beta DNMT3B (413-853) and DNA methyltransferase 3-like DNMT3L (178-379) Sample: DNA methyltransferase 3-like (178-379) dimer, 47 kDa Homo sapiens protein DNA methyltransferase 3 beta (413-853) dimer, 100 kDa Homo sapiens protein Buffer: 20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol, pH: 8 Experiment: SAXS data collected at 13A, Taiwan Photon Source, NSRRC on 2022 Nov 2 RgGuinier 4.5 nm Dmax 15.9 nm VolumePorod 191 nm3

SASDVM9 – Human DNA methyltransferase 3 beta DNMT3B (413-853) and DNA methyltransferase 3-like DNMT3L (178-379) in complex with histone H3 Sample: Histone H3.3 dimer, 8 kDa Homo sapiens protein DNA methyltransferase 3-like (178-379) dimer, 47 kDa Homo sapiens protein DNA methyltransferase 3 beta (413-853) dimer, 100 kDa Homo sapiens protein Buffer: 20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol, pH: 8 Experiment: SAXS data collected at 13A, Taiwan Photon Source, NSRRC on 2022 Nov 2 RgGuinier 4.5 nm Dmax 16.0 nm VolumePorod 186 nm3

SASDV29 – Complex of human DNA methyltransferase 3 beta DNMT3B (215-853) and DNA methyltransferase 3-like DNMT3L (178-379) Sample: DNA methyltransferase 3 beta (215-853) dimer, 145 kDa Homo sapiens protein DNA methyltransferase 3-like (178-379) dimer, 47 kDa Homo sapiens protein Buffer: 20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol, pH: 8 Experiment: SAXS data collected at 13A, Taiwan Photon Source, NSRRC on 2021 Apr 16 RgGuinier 5.2 nm Dmax 21.2 nm VolumePorod 271263 nm3

SASDVJ9 – Human DNA methyltransferase 3 beta DNMT3B (215-853) and DNA methyltransferase 3-like DNMT3L (178-379) in complex with histone H3 Sample: Histone H3.3 dimer, 8 kDa Homo sapiens protein DNA methyltransferase 3 beta (215-853) dimer, 145 kDa Homo sapiens protein Buffer: 20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol, pH: 8 Experiment: SAXS data collected at 13A, Taiwan Photon Source, NSRRC on 2021 Apr 16 RgGuinier 5.1 nm Dmax 18.9 nm VolumePorod 275 nm3