Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Nucleosome spacing regulates linker methylation by DNMT3A2/3B3.
Journal, issue, pages	Mol Cell, Vol. 86, Issue 5, Page 834-850.e9, Year 2026
Publish date	Mar 5, 2026
Authors	Xiaoyan Xie / Minmin Liu / Gabriella N L Chua / X Edward Zhou / Michelle L Dykstra / Shixin Liu / Peter A Jones / Evan J Worden /
PubMed Abstract	De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get ...De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get targeted by DNMT3 enzymes are not understood. We show that nucleosome spacing controls linker DNA methylation and H3K36me2 recognition by human DNMT3A2/3B3, linking de novo methylation to chromatin architecture. We present structures of DNMT3A2/3B3 bound to dinucleosomes, revealing that short linkers promote dinucleosome bridging, blocking access to linker DNA and suppressing methylation, whereas long linkers allow DNMT3A2/3B3 to engage each nucleosome separately and methylate linker DNA. Finally, we show that DNMT3A2/3B3 positions proline-tryptophan-tryptophan-proline (PWWP) domains to scan for H3K36me2. However, H3K36me2 recognition is blocked when DNMT3A2/3B3 bridges dinucleosomes with short linkers, imposing an additional structural constraint on DNMT3A2/3B3 function. Together, these findings uncover the mechanisms that govern de novo methylation in chromatin and explain how DNMT3 enzymes target linkers in cells.
External links	Mol Cell / PubMed:41742418 / PubMed Central
Methods	EM (single particle)
Resolution	3.14 - 8.0 Å
Structure data	47344 9e00 EMDB-47344, PDB-9e00: Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Method: EM (single particle) / Resolution: 3.75 Å 47349 9e05 EMDB-47349, PDB-9e05: The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Method: EM (single particle) / Resolution: 8.0 Å 47353 9e09 EMDB-47353, PDB-9e09: Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Method: EM (single particle) / Resolution: 3.72 Å 47354 9e0f EMDB-47354, PDB-9e0f: A focus of DNMT tetramer (1) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Method: EM (single particle) / Resolution: 3.46 Å 47355 9e0g EMDB-47355, PDB-9e0g: A focus of tetramer (2) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Method: EM (single particle) / Resolution: 3.72 Å 47448 9e2d EMDB-47448, PDB-9e2d: Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Method: EM (single particle) / Resolution: 6.08 Å 47450 9e2f EMDB-47450, PDB-9e2f: Cryo-EM structure of a di-nucleosome with a five base pair linker Method: EM (single particle) / Resolution: 5.9 Å 47461 9e2q EMDB-47461, PDB-9e2q: Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Method: EM (single particle) / Resolution: 3.14 Å 47462 9e2r EMDB-47462, PDB-9e2r: Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Method: EM (single particle) / Resolution: 7.71 Å 47479 9e3d EMDB-47479, PDB-9e3d: Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Method: EM (single particle) / Resolution: 3.8 Å 47495 9e3r EMDB-47495, PDB-9e3r: Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Method: EM (single particle) / Resolution: 6.9 Å 47499 9e49 EMDB-47499, PDB-9e49: Cryo-EM structure of a di-nucleosome with an eight base-pair linker Method: EM (single particle) / Resolution: 5.93 Å EMDB-71301: Consensus map for Cryo-EM structure of DNMT3A2/3B3 tetramer in complex with a 167H3K36me2 nucleosome Method: EM (single particle) / Resolution: 3.63 Å EMDB-71302: Focus map of DNMT3A2/3B3 tetramer for Cryo-EM structure of DNMT3A2/3B3 in complex with 167H3K36me2-nucleosome Method: EM (single particle) / Resolution: 6.35 Å EMDB-71304: Focus map of PWWP_1 domain for Cryo-EM structure of DNMT3A2/3B3 in complex with 167H3K36me2-nucleosome Method: EM (single particle) / Resolution: 4.91 Å EMDB-71305: Focus map of PWWP_2 for Cryo-EM structure of DNMT3A2/3B3 in complex with 167H3K36me2-nucleosome Method: EM (single particle) / Resolution: 5.86 Å EMDB-71306: Focus map of nucleosome for Cryo-EM structure of DNMT3A2/3B3 in complex with 167H3K36me2-nucleosome Method: EM (single particle) / Resolution: 4.43 Å EMDB-71604: Consensus map for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight-base-pair linker Method: EM (single particle) / Resolution: 3.84 Å EMDB-71605: Focus map of DNMT3A2/3B3 tetramer1 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Method: EM (single particle) / Resolution: 4.89 Å EMDB-71606: Focus map of DNMT3A2/3B3 tetramer2 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Method: EM (single particle) / Resolution: 5.51 Å EMDB-71607: Focus map of nucleosome 1 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Method: EM (single particle) / Resolution: 4.99 Å EMDB-71608: Focus map of nucleosome 2 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Method: EM (single particle) / Resolution: 3.51 Å EMDB-71609: Focus map of nucleosome1_PWWP1 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Method: EM (single particle) / Resolution: 4.99 Å 72318 9q7u EMDB-72318, PDB-9q7u: Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Method: EM (single particle) / Resolution: 3.4 Å 72487 9y4p EMDB-72487, PDB-9y4p: Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Method: EM (single particle) / Resolution: 3.84 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-SAH: S-ADENOSYL-L-HOMOCYSTEINE ChemComp-SAO: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
Source	homo sapiens (human) xenopus laevis (African clawed frog)
Keywords	DNA BINDING PROTEIN / DNMT3A2 / DNMT3B3 / DNA methylation / di-nucleosome / DNA BINDING PROTEIN/DNA / DNMT3A / DNMT3B / nucleosome / DNA BINDING PROTEIN-DNA complex / DNMT 3A2/3B3 / methylation / DNMT3A2-DNMT3B3 / 167H3K36me2-nucleosome / DNMT3A2/DNMT3B3 / H3K36me2 di-nucleosome