← Back to search
6w89

Structure of DNMT3A (R882H) in complex with CGA DNA

Method: X-RAY DIFFRACTION Dmax: 190.1 Å Quality: GOOD
▼

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

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–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts Chain A； UniProt 628–912 Chain D； UniProt 628–912 Not recorded DNA (cytosine-5)-methyltransferase 3-like × 2 （Q9UJW3） CGA DNA (25-MER) × 2 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
2 Protein–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts Chain G； UniProt 628–912 Chain J； UniProt 628–912 Not recorded DNA (cytosine-5)-methyltransferase 3-like × 2 （Q9UJW3） CGA DNA (25-MER) × 2 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

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 6W89 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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 construct 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 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
6W8B Structure of DNMT3A in complex with CGA DNA Deposited 2020-03-20 Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 method 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 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 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 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 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 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 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 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 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 method 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 method 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 construct 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 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
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 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 K 224–912（689 aa）
Chain W 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 3.72 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 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 construct 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 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 experimental method Different experimental conditions 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 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 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 method 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 method 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 method 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 construct 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 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 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 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 construct 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 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 experimental method Different experimental conditions 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 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNM3A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–285； UniProt 628–912 Author chain D； PDBConstruct 1–285； UniProt 628–912 Author chain G； PDBConstruct 1–285； UniProt 628–912 Author chain J； PDBConstruct 1–285； UniProt 628–912

DNA (cytosine-5)-methyltransferase 3-like

Homo sapiens

UniProt Q9UJW3

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–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts Chain B； UniProt 178–386 Chain C； UniProt 178–386 Not recorded DNA (cytosine-5)-methyltransferase 3A × 2 （Q9Y6K1） CGA DNA (25-MER) × 2 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
2 Protein–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts Chain H； UniProt 178–386 Chain I； UniProt 178–386 Not recorded DNA (cytosine-5)-methyltransferase 3A × 2 （Q9Y6K1） CGA DNA (25-MER) × 2 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

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 6W89 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2PV0 DNA methyltransferase 3 like protein (DNMT3L) Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–387（387 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；0.4-0.6 M sodium citrate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；12% polyethylene 3350, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.30 Å R-free 0.272
2PV0 DNA methyltransferase 3 like protein (DNMT3L) Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–387（387 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；0.4-0.6 M sodium citrate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；12% polyethylene 3350, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.30 Å R-free 0.272
2PV0 DNA methyltransferase 3 like protein (DNMT3L) Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–387（387 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；0.4-0.6 M sodium citrate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；12% polyethylene 3350, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.30 Å R-free 0.272
2PVC DNMT3L recognizes unmethylated histone H3 lysine 4 Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–387（387 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；300 K；12 % polyethylene glycol, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50
Resolution 3.69 Å R-free 0.302
2PVC DNMT3L recognizes unmethylated histone H3 lysine 4 Deposited 2007-05-09 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 1–387（387 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；300 K；12 % polyethylene glycol, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50
Resolution 3.69 Å R-free 0.302
2PVC DNMT3L recognizes unmethylated histone H3 lysine 4 Deposited 2007-05-09 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 C 1–387（387 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；300 K；12 % polyethylene glycol, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50
Resolution 3.69 Å R-free 0.302
2QRV Structure of Dnmt3a-Dnmt3L C-terminal domain complex Deposited 2007-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 160–387（228 aa） Fragment：residues 160 to 386
Chain C 160–387（228 aa） Fragment：residues 160 to 386
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 160–387（228 aa） Fragment：residues 160 to 386
Chain G 160–387（228 aa） Fragment：residues 160 to 386
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
4U7P Crystal structure of DNMT3A-DNMT3L complex Deposited 2014-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 178–379（202 aa） Fragment：UNP residues 178-379
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 178–379（202 aa） Fragment：UNP residues 178-379
Chain D 178–379（202 aa） Fragment：UNP residues 178-379
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–385（208 aa）
Chain C 178–385（208 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–387（210 aa）
Chain C 178–387（210 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 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 178–386（209 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 conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain C 178–386（209 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
6KDA Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site Deposited 2019-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–379（202 aa）
Chain C 178–379（202 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–379（202 aa）
Chain C 178–379（202 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 178–379（202 aa）
Chain C 178–379（202 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 178–379（202 aa）
Chain C 178–379（202 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 178–379（202 aa）
Chain C 178–379（202 aa）
Not recorded 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 B 178–379（202 aa）
Not recorded 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 C 178–379（202 aa）
Not recorded 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
6U8P Crystal structure of DNMT3B-DNMT3L in complex with CpGpA DNA Deposited 2019-09-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 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 2.95 Å R-free 0.236
6U8X Crystal structure of DNMT3B-DNMT3L in complex with CpApG DNA Deposited 2019-09-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 aa）
Not recorded 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 aa）
Not recorded 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
6W8B Structure of DNMT3A in complex with CGA DNA Deposited 2020-03-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 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 ligand/ion Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain I 178–386（209 aa）
Chain J 178–386（209 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 ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 178–386（209 aa）
Chain C 178–386（209 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
7X9D DNMT3B in complex with harmine Deposited 2022-03-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 178–379（202 aa）
Chain C 178–379（202 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
8TCI Crystal structure of DNMT3C-DNMT3L in complex with CGG DNA Deposited 2023-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 181–379（199 aa） Fragment：UNP residues 181-379
Chain C 181–379（199 aa） Fragment：UNP residues 181-379
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2% v/v Tacsimate, pH 8.0, 0.1 M Tris, pH 8.5, 16% w/v PEG3350
Resolution 3.19 Å R-free 0.257
8XEE Human DNMT3B mutant-R823G Deposited 2023-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 178–379（202 aa）
Chain C 178–379（202 aa）
Not recorded 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
9MP0 The cryo-EM structure of the human DNA methyltransferases DNMT3A2 and DNMT3L dodecamer Deposited 2024-12-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain P 1–386（386 aa）
Chain Q 1–386（386 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
9MPP The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Deposited 2024-12-31 Different construct 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 L 1–386（386 aa）
Chain N 1–386（386 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 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 B 1–386（386 aa）
Chain C 1–386（386 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

28 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNM3L_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–209； UniProt 178–386 Author chain C； PDBConstruct 1–209； UniProt 178–386 Author chain H； PDBConstruct 1–209； UniProt 178–386 Author chain I； PDBConstruct 1–209； UniProt 178–386

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 6w89

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6w89
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6w89
Deposition date deposition_date2020-03-20
Structure title titleStructure of DNMT3A (R882H) in complex with CGA DNA
Keywords keywordsDNA methylation, DNMT3A(R882H), AML, epigenetics, TRANSFERASE, TRANSFERASE-DNA complex; TRANSFERASE/DNA
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier49.75 Å
Radius of gyration Rg (electron density) rg_electron50.86 Å
Forward intensity I(0) i0967924000.00
Molecular weight molecular_weight239390.0 kDa
Excluded volume excluded_volume291260 ų
Envelope volume envelope_volume417870 ų
Hydration-shell volume shell_volume72533 ų
Envelope diameter envelope_diameter206.8 Å
Shell Rg shell_rg50.18 Å
Envelope Rg envelope_rg51.70 Å
Shape Rg shape_rg50.97 Å
Total Rg total_rg50.48 Å
Total atoms total_atoms16786
Residues n_residues1984
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
▼

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

Maximum dimension Dmax dmax190.1 Å
Rg (real space) rg_real50.42 Å
Rg uncertainty (real space) rg_real_error2.48 Å
I(0) (real space) i0_real9.6790e+08
I(0) uncertainty (real space) i0_real_error2.0470e+07
Rg (reciprocal space) rg_reciprocal49.75 Å
I(0) (reciprocal space) i0_reciprocal967100000.0000
Solution quality estimate total_estimate0.8051
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary53.5 Å
Skewness Skewness skewness0.663
Kurtosis Kurtosis kurtosis0.220
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha55400000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.585; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.794; Smooth: 0.913
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6w89B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id6w89C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id6w89H00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id6w89I00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
▶

8. Citations (1)

▶

9. Files and Curves (10)