← Back to search

Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q9UBC3 New Search
46PDB entries
56Biological assembly
128chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3FLG The PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 beta Deposited 2008-12-18 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric（15） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.