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9e0g

A focus of tetramer (2) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome

Method: ELECTRON MICROSCOPY Dmax: 147.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 3 of DNA (cytosine-5)-methyltransferase 3B

Homo sapiens

UniProt Q9UBC3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain L； UniProt 1–770 Chain X； UniProt 1–770 Not recorded DNA (cytosine-5)-methyltransferase 3A × 2 （Q9Y6K1） ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.72 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9E0G Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FLG The PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 beta Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 206–355（150 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；Purified DNMT3B was crystallized using sitting drop vapor diffusion method at 20 C by mixing 1 ul of the protein solution with 1 ul of the reservoir solution containing 30% PEG 2,000 MME, 0.2 M KBr, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.80 Å R-free 0.244
5CIU Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain Deposited 2015-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 206–355（150 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；1.6M SODIUM CITRATE TRIBASIC
Resolution 2.24 Å R-free 0.259
5CIU Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain Deposited 2015-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 206–355（150 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；1.6M SODIUM CITRATE TRIBASIC
Resolution 2.24 Å R-free 0.259
5NR3 Human DNMT3B PWWP domain in complex with ethambutol Deposited 2017-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–367（150 aa） Fragment：UNP residues 218-367
Not recorded 95E Ethambutol × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.30 Å R-free 0.238
5NR3 Human DNMT3B PWWP domain in complex with ethambutol Deposited 2017-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 218–367（150 aa） Fragment：UNP residues 218-367
Not recorded 95E Ethambutol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.30 Å R-free 0.238
5NRR Human DNMT3B PWWP domain in complex with 5-[(2-Hydroxyethyl)(propyl)amino]-1-pentanol Deposited 2017-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 218–367（150 aa）
Chain B 218–367（150 aa）
Not recorded 96E 5-[2-hydroxyethyl(propyl)amino]pentan-1-ol × 2 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES sodium, 2% v/v Polyethylene glycol 400, 2.0 M Ammonium sulfate
Resolution 1.70 Å R-free 0.213
5NRS Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine Deposited 2017-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 206–355（150 aa）
Chain B 206–355（150 aa）
Not recorded SO4 SULFATE ION × 5 962 (2~{S})-1-[2-hydroxyethyl-[(2~{S})-2-oxidanylpropyl]amino]propan-2-ol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.30 Å R-free 0.248
5NRV Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol Deposited 2017-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 218–367（150 aa）
Chain D 218–367（150 aa）
Not recorded 96K 6-dipropylamino-1-hexanol × 2 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.08 Å R-free 0.243
5NV0 Human DNMT3B PWWP domain in complex with 4-(dipropylamino)butyronitrile Deposited 2017-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 206–355（150 aa）
Chain B 206–355（150 aa）
Not recorded 9AH 4-(dipropylamino)butanenitrile × 2 SO4 SULFATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.40 Å R-free 0.243
5NV2 Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S) Deposited 2017-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 206–355（150 aa）
Chain B 206–355（150 aa）
Not recorded 9AE (2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.03 Å R-free 0.240
5NV7 Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 206–355（150 aa）
Not recorded 9AK N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.57 Å R-free 0.233
5NV7 Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 206–355（150 aa）
Not recorded 9AK N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.57 Å R-free 0.233
5NVO Human DNMT3B PWWP domain in complex with choline Deposited 2017-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–367（150 aa）
Not recorded CHT CHOLINE ION × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.40 Å R-free 0.244
5NVO Human DNMT3B PWWP domain in complex with choline Deposited 2017-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 218–367（150 aa）
Not recorded CHT CHOLINE ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Resolution 2.40 Å R-free 0.244
6KDA Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site Deposited 2019-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 571–853（283 aa）
Chain D 571–853（283 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0 mM MES (pH 5.7), 160 mM KCl, 10 mM MgSO4 and 14% PEG 400
Resolution 2.91 Å R-free 0.220
6KDB Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpT site Deposited 2019-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 571–853（283 aa）
Chain D 571–853（283 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；50 mM MES (pH 5.6), 200 mM KCl, 10 mM MgSO4, 10% PEG 400
Resolution 2.86 Å R-free 0.202
6KDL Crystal structure of human DNMT3B-DNMT3L complex (I) Deposited 2019-07-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 571–853（283 aa）
Chain D 571–853（283 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；278 K；20 mM Tris-HCl (pH 7.4), 200 mM NaCl, 5% glycerol, and 0.5 mM TCEP
Resolution 3.27 Å R-free 0.212
6KDP Crystal structure of human DNMT3B-DNMT3L complex (II) Deposited 2019-07-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 571–853（283 aa）
Chain D 571–853（283 aa）
Not recorded FMT FORMIC ACID × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；2.7 M Sodium formate
Resolution 2.93 Å R-free 0.244
6KDT Crystal structure of human DNMT3B (Q772R)-DNMT3L complex Deposited 2019-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 571–853（283 aa）
Chain D 571–853（283 aa）
Mutation：Q772R Mutation：Q772R SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；2.2 M sodium formate
Resolution 2.87 Å R-free 0.242
6KDT Crystal structure of human DNMT3B (Q772R)-DNMT3L complex Deposited 2019-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 571–853（283 aa）
Mutation：Q772R SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；2.2 M sodium formate
Resolution 2.87 Å R-free 0.242
6KDT Crystal structure of human DNMT3B (Q772R)-DNMT3L complex Deposited 2019-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 571–853（283 aa）
Mutation：Q772R SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；2.2 M sodium formate
Resolution 2.87 Å R-free 0.242
6PA7 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Deposited 2019-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain N 1–770（770 aa）
Chain S 1–770（770 aa）
Not recorded CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
6R3E Human DNMT3B PWWP domain in complex with triisopropanolamine Deposited 2019-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 215–351（137 aa）
Chain A 139–275（137 aa）
Not recorded 96H Triisopropanolamine × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES, 0.2 M Li2SO4, 23-33% PEG3350
Resolution 2.27 Å R-free 0.264
6R3E Human DNMT3B PWWP domain in complex with triisopropanolamine Deposited 2019-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 215–351（137 aa）
Chain B 139–275（137 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M MES, 0.2 M Li2SO4, 23-33% PEG3350
Resolution 2.27 Å R-free 0.264
6U8P Crystal structure of DNMT3B-DNMT3L in complex with CpGpA DNA Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 563–853（291 aa）
Chain D 563–853（291 aa）
Not recorded MG MAGNESIUM ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289.15 K；0.1 M Tris-HCl (pH 8.0), 100 mM MgCl2, 7% PEG8000
Resolution 3.05 Å R-free 0.239
6U8V Crystal structure of DNMT3B-DNMT3L in complex with CpGpT DNA Deposited 2019-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 563–853（291 aa）
Chain D 563–853（291 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000
Resolution 3.00 Å R-free 0.249
6U8W Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA Deposited 2019-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 563–853（291 aa）
Chain D 563–853（291 aa）
Mutation：K777A Mutation：K777A SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000
Resolution 2.95 Å R-free 0.236
6U8X Crystal structure of DNMT3B-DNMT3L in complex with CpApG DNA Deposited 2019-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 563–853（291 aa）
Chain D 563–853（291 aa）
Not recorded MG MAGNESIUM ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289.15 K；0.1 M Tris-HCl (pH 8.0), 100 mM MgCl2, 7% PEG8000
Resolution 2.95 Å R-free 0.252
6U90 Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA Deposited 2019-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 563–853（291 aa）
Chain D 563–853（291 aa）
Mutation：N779A Mutation：N779A GOL GLYCEROL × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000
Resolution 3.00 Å R-free 0.259
6U91 Crystal structure of DNMT3B(Q772R)-DNMT3L in complex with CpGpT DNA Deposited 2019-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 563–853（291 aa）
Chain D 563–853（291 aa）
Mutation：Q772R Mutation：Q772R MG MAGNESIUM ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000
Resolution 3.00 Å R-free 0.259
7O45 Crystal structure of ADD domain of the human DNMT3B methyltransferase Deposited 2021-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 404–546（143 aa）
Chain B 404–546（143 aa）
Chain C 404–546（143 aa）
Not recorded ZN ZINC ION × 9 BR BROMIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.2M NaBr; 0.1M bis-tris-propane pH 7.5; 20% PEG 3350
Resolution 2.10 Å R-free 0.228
7O45 Crystal structure of ADD domain of the human DNMT3B methyltransferase Deposited 2021-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 404–546（143 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.2M NaBr; 0.1M bis-tris-propane pH 7.5; 20% PEG 3350
Resolution 2.10 Å R-free 0.228
7V0E Crystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain. Deposited 2022-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 569–853（285 aa）
Chain D 569–853（285 aa）
Chain E 569–853（285 aa）
Chain F 569–853（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M MES pH6.5, 1.4 M Ammonium sulfate, 0.2 mM AdoHcy and 8% v/v 1,4-Dioxane
Resolution 3.27 Å R-free 0.235
7V0E Crystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain. Deposited 2022-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 569–853（285 aa）
Chain C 569–853（285 aa）
Chain G 569–853（285 aa）
Chain H 569–853（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M MES pH6.5, 1.4 M Ammonium sulfate, 0.2 mM AdoHcy and 8% v/v 1,4-Dioxane
Resolution 3.27 Å R-free 0.235
7X9D DNMT3B in complex with harmine Deposited 2022-03-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 571–853（283 aa）
Chain D 571–853（283 aa）
Not recorded HRM 7-METHOXY-1-METHYL-9H-BETA-CARBOLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；bis-tris propane pH 7.0, sodium formate
Resolution 3.08 Å R-free 0.245
8EIH Cryo-EM structure of human DNMT3B homo-tetramer (form I) Deposited 2022-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 206–853（648 aa）
Chain B 206–853（648 aa）
Chain C 206–853（648 aa）
Chain D 206–853（648 aa）
Chain E 206–853（648 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8EII Cryo-EM structure of human DNMT3B homo-tetramer (form II) Deposited 2022-09-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 206–853（648 aa）
Chain B 206–853（648 aa）
Chain C 206–853（648 aa）
Chain D 206–853（648 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8EIJ Cryo-EM structure of human DNMT3B homo-trimer Deposited 2022-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 206–853（648 aa）
Chain B 206–853（648 aa）
Chain D 206–853（648 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8EIK Cryo-EM structure of human DNMT3B homo-hexamer Deposited 2022-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 206–853（648 aa）
Chain B 206–853（648 aa）
Chain C 206–853（648 aa）
Chain D 206–853（648 aa）
Chain E 206–853（648 aa）
Chain F 206–853（648 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 3 ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
8XEE Human DNMT3B mutant-R823G Deposited 2023-12-11 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 571–853（283 aa）
Chain D 571–853（283 aa）
Mutation：R823G Mutation：R823G SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；HEPES (pH 7.5), MgCl2, 2-methyl-2,4-pentanediol, spermine
Resolution 3.03 Å R-free 0.236
8ZLK PWWP domain from human DNMT3B Deposited 2024-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 206–355（150 aa） Fragment：PWWP domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；Lithium sulfate monohydrate, CAPS, Ammonium sulfate
Resolution 2.74 Å R-free 0.267
8ZLK PWWP domain from human DNMT3B Deposited 2024-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 206–355（150 aa） Fragment：PWWP domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；Lithium sulfate monohydrate, CAPS, Ammonium sulfate
Resolution 2.74 Å R-free 0.267
9E00 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 1–770（770 aa）
Chain V 1–770（770 aa）
Chain X 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9E05 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 1–770（770 aa）
Chain V 1–770（770 aa）
Chain X 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
9E09 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain V 819–829（11 aa）
Chain X 819–830（12 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
9E0F A focus of DNMT tetramer (1) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9E0R Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-18 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain K 819–829（11 aa）
Chain L 819–829（11 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E2D Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 1–770（770 aa）
Chain V 1–770（770 aa）
Chain X 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.08 Å
9E2Q Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 1–770（770 aa）
Chain V 1–770（770 aa）
Chain X 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9E2R Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 1–770（770 aa）
Chain V 1–770（770 aa）
Chain X 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.71 Å
9E3D Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Deposited 2024-10-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain V 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9E3R Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 1–770（770 aa）
Chain V 1–770（770 aa）
Chain X 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9E3U Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Deposited 2024-10-24 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain L 1–770（770 aa）
Chain V 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
9Q7U Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Deposited 2025-08-25 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain V 118–694（577 aa）
Chain Z 118–694（577 aa）
Not recorded ZN ZINC ION × 9 SAO 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9Y4P Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain Z 118–694（577 aa）
Chain b 118–694（577 aa）
Chain e 118–694（577 aa）
Chain g 118–694（577 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å

45 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNM3B_HUMAN
Isoform Q9UBC3-3
PDB entities 1
Chains and sequence ranges Author chain L； PDBConstruct 1–773； UniProt 1–770 Author chain X； PDBConstruct 1–773； UniProt 1–770

DNA (cytosine-5)-methyltransferase 3A

Homo sapiens

UniProt Q9Y6K1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain K； UniProt 224–912 Chain W； UniProt 224–912 Not recorded Isoform 3 of DNA (cytosine-5)-methyltransferase 3B × 2 （Q9UBC3） ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.72 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9E0G Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2QRV Structure of Dnmt3a-Dnmt3L C-terminal domain complex Deposited 2007-07-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 624–909（286 aa） Fragment：residues 623 to 908
Chain D 624–909（286 aa） Fragment：residues 623 to 908
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；300 K；The final protein solution CONTAINED ~100 TO 133 micro M COMPLEX IN 20 milli M TRIS/HCL, PH 8.0, 100 milli M NACL, 5 % GLYCEROL, AND 0.1 % MERCAPTOETHANOL. Crystals were obtained with the mother liquor containing 2~5 % PEG 3000, 100 mM Tris/HCl, pH 8.0, 5 % glycerol at 16C, VAPOR DIFFUSION, HANGING DROP
Resolution 2.89 Å R-free 0.281
2QRV Structure of Dnmt3a-Dnmt3L C-terminal domain complex Deposited 2007-07-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 624–909（286 aa） Fragment：residues 623 to 908
Chain H 624–909（286 aa） Fragment：residues 623 to 908
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；300 K；The final protein solution CONTAINED ~100 TO 133 micro M COMPLEX IN 20 milli M TRIS/HCL, PH 8.0, 100 milli M NACL, 5 % GLYCEROL, AND 0.1 % MERCAPTOETHANOL. Crystals were obtained with the mother liquor containing 2~5 % PEG 3000, 100 mM Tris/HCl, pH 8.0, 5 % glycerol at 16C, VAPOR DIFFUSION, HANGING DROP
Resolution 2.89 Å R-free 0.281
3A1A Crystal Structure of the DNMT3A ADD domain Deposited 2009-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 476–614（139 aa） Fragment：ADD(ATRX-DNMT3-DNMT3L) domain, residues 476-614
Not recorded ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；17% PEG 8000, 0.1M Tris-HCl, 0.2M magnesium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.250
3A1B Crystal structure of the DNMT3A ADD domain in complex with histone H3 Deposited 2009-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 476–614（139 aa） Fragment：ADD(ATRX-DNMT3-DNMT3L) domain(residues 476-614), UNP residues 2-21(Histone H3.1)
Not recorded ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 2000 monomethyl ether, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.29 Å R-free 0.224
3LLR Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha Deposited 2010-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 275–427（153 aa） Fragment：PWWP domain (UNP residues 275-427)
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；28% PEG 3,350, 0.1 M ammonium sulfate, 0.1M BisTris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.256
3LLR Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha Deposited 2010-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 275–427（153 aa） Fragment：PWWP domain (UNP residues 275-427)
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；28% PEG 3,350, 0.1 M ammonium sulfate, 0.1M BisTris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.256
3LLR Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha Deposited 2010-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 275–427（153 aa） Fragment：PWWP domain (UNP residues 275-427)
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；28% PEG 3,350, 0.1 M ammonium sulfate, 0.1M BisTris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.256
3LLR Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha Deposited 2010-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 275–427（153 aa） Fragment：PWWP domain (UNP residues 275-427)
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；28% PEG 3,350, 0.1 M ammonium sulfate, 0.1M BisTris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.256
3LLR Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha Deposited 2010-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 275–427（153 aa） Fragment：PWWP domain (UNP residues 275-427)
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；28% PEG 3,350, 0.1 M ammonium sulfate, 0.1M BisTris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.256
3SVM Human MPP8 - human DNMT3AK47me2 peptide Deposited 2011-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 40–53（14 aa） Fragment：unp residues 40-53
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；30% polyethylene glycol 1500, 20% polyethylene glycol 400 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.31 Å R-free 0.272
3SVM Human MPP8 - human DNMT3AK47me2 peptide Deposited 2011-07-12 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 40–53（14 aa） Fragment：unp residues 40-53
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；30% polyethylene glycol 1500, 20% polyethylene glycol 400 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.31 Å R-free 0.272
4QBQ Crystal structure of DNMT3a ADD domain bound to H3 peptide Deposited 2014-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 479–610（132 aa） Fragment：ADD Domain, UNP residues 476-611
Chain C 479–610（132 aa） Fragment：ADD Domain, UNP residues 476-611
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；29% PEGMME5000, 0.1M Bis-Tris Propane-HCL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.41 Å R-free 0.230
4QBR Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 476–611（136 aa） Fragment：ADD Domain, UNP residues 476-611
Mutation：G550D ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；25% PEG3350, 0.1M Bis-Tris-HCL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.225
4QBR Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 476–611（136 aa） Fragment：ADD Domain, UNP residues 476-611
Mutation：G550D ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；25% PEG3350, 0.1M Bis-Tris-HCL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.225
4QBS Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 476–611（136 aa） Fragment：ADD Domain, UNP residues 456-661
Mutation：E545R ZN ZINC ION × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG3350, 0.1M Bis-Tris, 0.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.203
4U7P Crystal structure of DNMT3A-DNMT3L complex Deposited 2014-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 455–912（458 aa） Fragment：UNP residues 455-912
Not recorded ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；291 K；0.05M Bis-Tris, 0.1M Sodium Malonate, 8% PEG3350
Resolution 3.82 Å R-free 0.269
4U7T Crystal structure of DNMT3A-DNMT3L in complex with histone H3 Deposited 2014-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 476–912（437 aa） Fragment：UNP residues 476-912
Chain C 476–912（437 aa） Fragment：UNP residues 476-912
Not recorded ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium Acetate, 0.6M Ammonium Sulfate
Resolution 2.90 Å R-free 0.261
5YX2 Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites Deposited 2017-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 628–912（285 aa）
Chain D 628–912（285 aa）
Not recorded GOL GLYCEROL × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M Tris-HCl (pH 7.0), 200 mM NaH2PO4, 5% PEG 4000
Resolution 2.65 Å R-free 0.222
6BRR Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites Deposited 2017-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 439–723（285 aa）
Chain D 439–723（285 aa）
Mutation：R836A Mutation：R836A SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Tris-HCl (pH 7.0), 200 mM NaH2PO4 and 5% PEG4000
Resolution 2.97 Å R-free 0.242
6F57 Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA Deposited 2017-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 628–912（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；7% PEG4000, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2, 166 mM imidazole (pH 7.0)
Resolution 3.10 Å R-free 0.242
6F57 Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA Deposited 2017-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain D 628–912（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；7% PEG4000, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2, 166 mM imidazole (pH 7.0)
Resolution 3.10 Å R-free 0.242
6PA7 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Deposited 2019-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 224–912（689 aa）
Chain P 224–912（689 aa）
Not recorded CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
6W89 Structure of DNMT3A (R882H) in complex with CGA DNA Deposited 2020-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 628–912（285 aa）
Chain D 628–912（285 aa）
Not recorded CIT CITRIC ACID × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000
Resolution 2.50 Å R-free 0.240
6W89 Structure of DNMT3A (R882H) in complex with CGA DNA Deposited 2020-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain G 628–912（285 aa）
Chain J 628–912（285 aa）
Not recorded CIT CITRIC ACID × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000
Resolution 2.50 Å R-free 0.240
6W8B Structure of DNMT3A in complex with CGA DNA Deposited 2020-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 628–912（285 aa）
Chain D 628–912（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000
Resolution 2.40 Å R-free 0.233
6W8B Structure of DNMT3A in complex with CGA DNA Deposited 2020-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain H 628–912（285 aa）
Chain K 628–912（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000
Resolution 2.40 Å R-free 0.233
6W8D Structure of DNMT3A (R882H) in complex with CGT DNA Deposited 2020-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 628–912（285 aa）
Chain D 628–912（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000
Resolution 2.60 Å R-free 0.253
6W8J Structure of DNMT3A (R882H) in complex with CAG DNA Deposited 2020-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 628–912（285 aa）
Chain D 628–912（285 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.4, 0.2 % PEG8000
Resolution 2.44 Å R-free 0.223
8BA5 Crystal structure of the DNMT3A ADD domain Deposited 2022-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 476–614（139 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291.15 K；17 % PEG 8000, 0.2 M Magnesiumsulfat, 0.1 M TRIS-HCl pH 7.5
Resolution 1.45 Å R-free 0.213
8QZM Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome Deposited 2023-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–912（912 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5, 65 mM NaCl, 1 mM DTT, 0.1 mM S-Adenosyl methionine
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TDR Crystal structure of the methyltransferase domain of DNMT3A homotetramer Deposited 2023-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain B 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain E 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain F 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 3.32 Å R-free 0.240
8TDR Crystal structure of the methyltransferase domain of DNMT3A homotetramer Deposited 2023-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain D 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain G 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain H 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 3.32 Å R-free 0.240
8TE1 Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A homotetramer Deposited 2023-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain B 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain E 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain F 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Mutation：R882H,R676K Mutation：R882H,R676K Mutation：R882H,R676K Mutation：R882H,R676K SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 2.48 Å R-free 0.226
8TE1 Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A homotetramer Deposited 2023-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain D 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain G 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain H 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Mutation：R882H,R676K Mutation：R882H,R676K Mutation：R882H,R676K Mutation：R882H,R676K SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 5 TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 2.48 Å R-free 0.226
8TE3 Crystal structure of the methyltransferase domain of R882C/R676K DNMT3A homotetramer Deposited 2023-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain B 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain E 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain F 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Mutation：R882C,R676K Mutation：R882C,R676K Mutation：R882C,R676K Mutation：R882C,R676K SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 3.20 Å R-free 0.241
8TE3 Crystal structure of the methyltransferase domain of R882C/R676K DNMT3A homotetramer Deposited 2023-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain D 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain G 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain H 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Mutation：R882C,R676K Mutation：R882C,R676K Mutation：R882C,R676K Mutation：R882C,R676K SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 3.20 Å R-free 0.241
8TE4 Crystal structure of the methyltransferase domain of R882H/N879A DNMT3A homotetramer Deposited 2023-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain B 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain E 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain F 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Mutation：R882H,N879A Mutation：R882H,N879A Mutation：R882H,N879A Mutation：R882H,N879A SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 2.65 Å R-free 0.236
8TE4 Crystal structure of the methyltransferase domain of R882H/N879A DNMT3A homotetramer Deposited 2023-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain D 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain G 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Chain H 628–912（285 aa） Fragment：methyltransferase domain (UNP residues 628-912)
Mutation：R882H,N879A Mutation：R882H,N879A Mutation：R882H,N879A Mutation：R882H,N879A SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.4 M potassium sodium tartrate
Resolution 2.65 Å R-free 0.236
8U5H Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Deposited 2023-09-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 126–223（98 aa）
Chain B 126–223（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8UW1 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Deposited 2023-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 159–228（70 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
9E00 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain K 224–912（689 aa）
Chain U 224–912（689 aa）
Chain W 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9E05 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain K 224–912（689 aa）
Chain U 224–912（689 aa）
Chain W 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
9E0F A focus of DNMT tetramer (1) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain U 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9E2D Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain K 224–912（689 aa）
Chain U 224–912（689 aa）
Chain W 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.08 Å
9E2Q Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain K 224–912（689 aa）
Chain U 224–912（689 aa）
Chain W 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9E2R Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain K 224–912（689 aa）
Chain U 224–912（689 aa）
Chain W 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.71 Å
9E3D Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Deposited 2024-10-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain U 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9E3R Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain K 224–912（689 aa）
Chain U 224–912（689 aa）
Chain W 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9E3U Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Deposited 2024-10-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain U 224–912（689 aa）
Chain Y 224–912（689 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
9LQ1 Structure of human DNMT3A-TCL1A complex Deposited 2025-01-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–912（912 aa）
Chain F 1–912（912 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out in argon atmosphere
Resolution 3.36 Å
9MP0 The cryo-EM structure of the human DNA methyltransferases DNMT3A2 and DNMT3L dodecamer Deposited 2024-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain L 224–912（689 aa）
Chain M 224–912（689 aa）
Chain N 224–912（689 aa）
Chain O 224–912（689 aa）
Chain R 224–912（689 aa）
Chain S 224–912（689 aa）
Chain T 224–912（689 aa）
Chain U 224–912（689 aa）
Not recorded ZN ZINC ION × 30 SAH S-ADENOSYL-L-HOMOCYSTEINE × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9MPO The cryo-EM structure of the human DNA methyltransferase DNMT3A2 and DNMT3L octamer Deposited 2024-12-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 224–912（689 aa）
Chain B 224–912（689 aa）
Chain C 224–912（689 aa）
Chain D 224–912（689 aa）
Chain E 224–912（689 aa）
Chain F 224–912（689 aa）
Not recorded ZN ZINC ION × 12 SAH S-ADENOSYL-L-HOMOCYSTEINE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9MPP The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Deposited 2024-12-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain K 224–912（689 aa）
Chain M 224–912（689 aa）
Not recorded ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9PRW Cryo-EM structure of human DNMT3A/3L Deposited 2025-07-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 281–912（632 aa）
Chain D 281–912（632 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9Q7U Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Deposited 2025-08-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain K 224–912（689 aa）
Chain L 224–912（689 aa）
Not recorded ZN ZINC ION × 9 SAO 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9Y4P Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain a 224–912（689 aa）
Chain c 224–912（689 aa）
Chain d 224–912（689 aa）
Chain f 224–912（689 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å

42 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNM3A_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain K； PDBConstruct 1–689； UniProt 224–912 Author chain W； PDBConstruct 1–689； UniProt 224–912

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9e0g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9e0g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9e0g
Deposition date deposition_date2024-10-17
Structure title titleA focus of tetramer (2) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome
Keywords keywordsDNMT3A2, DNMT3B3, DNA methylation, di-nucleosome, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier45.45 Å
Radius of gyration Rg (electron density) rg_electron45.36 Å
Forward intensity I(0) i0453885000.00
Molecular weight molecular_weight173630.0 kDa
Excluded volume excluded_volume216320 ų
Envelope volume envelope_volume337510 ų
Hydration-shell volume shell_volume61562 ų
Envelope diameter envelope_diameter155.8 Å
Shell Rg shell_rg50.65 Å
Envelope Rg envelope_rg44.59 Å
Shape Rg shape_rg45.38 Å
Total Rg total_rg45.55 Å
Total atoms total_atoms12159
Residues n_residues1507
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax147.3 Å
Rg (real space) rg_real45.41 Å
Rg uncertainty (real space) rg_real_error1.20 Å
I(0) (real space) i0_real4.5390e+08
I(0) uncertainty (real space) i0_real_error8.6860e+06
Rg (reciprocal space) rg_reciprocal45.45 Å
I(0) (reciprocal space) i0_reciprocal453900000.0000
Solution quality estimate total_estimate0.8948
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary58.9 Å
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.554
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha41390000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.811
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)