8tdr

Crystal structure of the methyltransferase domain of DNMT3A homotetramer

Method: X-RAY DIFFRACTION D_max: 192.2 Å Quality: REASONABLE

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

DNA (cytosine-5)-methyltransferase 3A

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 628–912 Chain B； UniProt 628–912 Chain E； UniProt 628–912 Chain F； UniProt 628–912	Fragment：methyltransferase domain (UNP residues 628-912)	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 628–912 Chain D； UniProt 628–912 Chain G； UniProt 628–912 Chain H； UniProt 628–912	Fragment：methyltransferase domain (UNP residues 628-912)	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

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 8TDR	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 628–912（285 aa） Chain D 628–912（285 aa）	Not recorded	GOL GLYCEROL × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M Tris-HCl (pH 7.0), 200 mM NaH2PO4, 5% PEG 4000	Resolution 2.65 Å R-free 0.222
6BRR Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites Deposited 2017-11-30	Different construct Different mutation/modification Different oligomeric state Different 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain K 224–912（689 aa） Chain P 224–912（689 aa）	Not recorded	CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
6W89 Structure of DNMT3A (R882H) in complex with CGA DNA Deposited 2020-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 628–912（285 aa） Chain D 628–912（285 aa）	Not recorded	CIT CITRIC ACID × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000	Resolution 2.50 Å R-free 0.240
6W89 Structure of DNMT3A (R882H) in complex with CGA DNA Deposited 2020-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain G 628–912（285 aa） Chain J 628–912（285 aa）	Not recorded	CIT CITRIC ACID × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000	Resolution 2.50 Å R-free 0.240
6W8B Structure of DNMT3A in complex with CGA DNA Deposited 2020-03-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 628–912（285 aa） Chain D 628–912（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000	Resolution 2.40 Å R-free 0.233
6W8B Structure of DNMT3A in complex with CGA DNA Deposited 2020-03-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain H 628–912（285 aa） Chain K 628–912（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000	Resolution 2.40 Å R-free 0.233
6W8D Structure of DNMT3A (R882H) in complex with CGT DNA Deposited 2020-03-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 628–912（285 aa） Chain D 628–912（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Sodium Citrate pH 4.2, 1% PEG8000	Resolution 2.60 Å R-free 0.253
6W8J Structure of DNMT3A (R882H) in complex with CAG DNA Deposited 2020-03-20	Different construct Different mutation/modification Different oligomeric state 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
8TE1 Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A homotetramer Deposited 2023-07-05	Different mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification 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 mutation/modification 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain 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 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain 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 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 3–287； UniProt 628–912 Author chain B； PDBConstruct 3–287； UniProt 628–912 Author chain C； PDBConstruct 3–287； UniProt 628–912 Author chain D； PDBConstruct 3–287； UniProt 628–912 Author chain E； PDBConstruct 3–287； UniProt 628–912 Author chain F； PDBConstruct 3–287； UniProt 628–912 Author chain G； PDBConstruct 3–287； UniProt 628–912 Author chain H； PDBConstruct 3–287； UniProt 628–912

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tdr
Deposition date deposition_date	2023-07-04
Structure title title	Crystal structure of the methyltransferase domain of DNMT3A homotetramer
Keywords keywords	DNA Methyltransferase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	57.34 Å
Radius of gyration Rg (electron density) rg_electron	58.51 Å
Forward intensity I(0) i0	583327000.00
Molecular weight molecular_weight	203480.0 kDa
Excluded volume excluded_volume	255620 Å³
Envelope volume envelope_volume	397850 Å³
Hydration-shell volume shell_volume	61988 Å³
Envelope diameter envelope_diameter	214.3 Å
Shell Rg shell_rg	52.75 Å
Envelope Rg envelope_rg	58.17 Å
Shape Rg shape_rg	58.52 Å
Total Rg total_rg	58.30 Å
Total atoms total_atoms	14355
Residues n_residues	1820
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	192.2 Å
Rg (real space) rg_real	58.13 Å
Rg uncertainty (real space) rg_real_error	2.35 Å
I(0) (real space) i0_real	5.8330e+08
I(0) uncertainty (real space) i0_real_error	1.2080e+07
Rg (reciprocal space) rg_reciprocal	56.64 Å
I(0) (reciprocal space) i0_reciprocal	582000000.0000
Solution quality estimate total_estimate	0.7390
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.6 Å
Skewness Skewness skewness	0.541
Kurtosis Kurtosis kurtosis	-0.465
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26690000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.497; Smooth: 0.078

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	179.429 Å
Unit-cell length b length_b	179.429 Å
Unit-cell length c length_c	108.065 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	3.320 Å
Low-resolution limit resolution_low	46.290 Å
R factor r_factor	0.2108
R_work r_work	0.2097
R_free r_free	0.2396

Description description	DNA (cytosine-5)-methyltransferase 3A
Molecular weight formula_weight	32859.8 kDa
EC 编号 ec_number	2.1.1.37,2.1.1.-
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,E,H,F,D,G
Atom count atom_count	14431

Crystal structure of the methyltransferase domain of DNMT3A homotetramer

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

DNA (cytosine-5)-methyltransferase 3A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	4

fit	/app/data/saxs_computation/td/8tdr/8tdr.fit
pddf	/app/data/pr_computation/td/8tdr/8tdr.pr.out
profile	/app/data/saxs_computation/td/8tdr/8tdr.dat