7o45

Crystal structure of ADD domain of the human DNMT3B methyltransferase

Method: X-RAY DIFFRACTION D_max: 74.9 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 6 of DNA (cytosine-5)-methyltransferase 3B

Homo sapiens

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 404–546 Chain B； UniProt 404–546 Chain C； UniProt 404–546	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 404–546	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

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 7O45	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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 × 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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
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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 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 × 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
9E0G A focus of tetramer (2) 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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 1–770（770 aa） Chain X 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 3.72 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 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 × 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 experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DNM3B_HUMAN
Isoform	Q9UBC3-6
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–146； UniProt 404–546 Author chain B； PDBConstruct 4–146； UniProt 404–546 Author chain C； PDBConstruct 4–146； UniProt 404–546 Author chain D； PDBConstruct 4–146； UniProt 404–546

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7o45
Deposition date deposition_date	2021-04-05
Structure title title	Crystal structure of ADD domain of the human DNMT3B methyltransferase
Keywords keywords	Methyltransferase 3B, DNA methylation, DNMT3B, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.18 Å
Radius of gyration Rg (electron density) rg_electron	24.04 Å
Forward intensity I(0) i0	66859100.00
Molecular weight molecular_weight	57305.0 kDa
Excluded volume excluded_volume	68834 Å³
Envelope volume envelope_volume	88226 Å³
Hydration-shell volume shell_volume	30030 Å³
Envelope diameter envelope_diameter	76.5 Å
Shell Rg shell_rg	31.88 Å
Envelope Rg envelope_rg	24.13 Å
Shape Rg shape_rg	24.03 Å
Total Rg total_rg	24.91 Å
Total atoms total_atoms	3912
Residues n_residues	507
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	74.9 Å
Rg (real space) rg_real	25.02 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	6.6860e+07
I(0) uncertainty (real space) i0_real_error	8.3520e+05
Rg (reciprocal space) rg_reciprocal	25.07 Å
I(0) (reciprocal space) i0_reciprocal	66860000.0000
Solution quality estimate total_estimate	0.9110
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.5 Å
Skewness Skewness skewness	0.038
Kurtosis Kurtosis kurtosis	-0.615
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12740000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
Molecular weight formula_weight	16556.7 kDa
EC 编号 ec_number	2.1.1.37
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4065

SGSDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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8. Citations (1)

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Unit-cell length a length_a	80.282 Å
Unit-cell length b length_b	89.943 Å
Unit-cell length c length_c	92.195 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	64.380 Å
R factor r_factor	0.2015
R_work r_work	0.2000
R_free r_free	0.2281

fit	/app/data/saxs_computation/o4/7o45/7o45.fit
pddf	/app/data/pr_computation/o4/7o45/7o45.pr.out
profile	/app/data/saxs_computation/o4/7o45/7o45.dat