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- PDB-4u7p: Crystal structure of DNMT3A-DNMT3L complex -

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Basic information

Entry
Database: PDB / ID: 4u7p
TitleCrystal structure of DNMT3A-DNMT3L complex
Components
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3A
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / DNA methyltransferase / autoinhibitory form / TRANSFERASE-TRANSFERASE REGULATOR complex
Function / homology
Function and homology information


epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / cellular response to bisphenol A ...epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / XY body / response to vitamin A / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / hepatocyte apoptotic process / lncRNA binding / negative regulation of gene expression, epigenetic / male meiosis I / cellular response to ethanol / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / placenta development / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / response to cocaine / stem cell differentiation / cellular response to amino acid stimulus / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / enzyme activator activity / euchromatin / response to lead ion / response to toxic substance / nuclear matrix / RMTs methylate histone arginines / neuron differentiation / transcription corepressor activity / response to estradiol / spermatogenesis / methylation / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Vaccinia Virus protein VP39 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3-like / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.821 Å
AuthorsWang, L. / Guo, X. / Li, J. / Xiao, J. / Yin, X. / He, S. / Wang, J. / Xu, Y.
CitationJournal: Nature / Year: 2015
Title: Structural insight into autoinhibition and histone H3-induced activation of DNMT3A
Authors: Guo, X. / Wang, L. / Li, J. / Ding, Z. / Xiao, J. / Yin, X. / He, S. / Shi, P. / Dong, L. / Li, G. / Tian, C. / Wang, J. / Cong, Y. / Xu, Y.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0516
Polymers77,4702
Non-polymers5814
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-6 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.031, 252.031, 75.336
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Detailsbiological unit is the same as asym.

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3A / DNA methyltransferases DNMT3A


Mass: 53350.352 Da / Num. of mol.: 1 / Fragment: UNP residues 455-912
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like / DNA methyltransferases DNMT3L


Mass: 24119.654 Da / Num. of mol.: 1 / Fragment: UNP residues 178-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJW3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6 / Details: 0.05M Bis-Tris, 0.1M Sodium Malonate, 8% PEG3350 / PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2816 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2013
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2816 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Number: 80080 / Rmerge(I) obs: 0.098 / Χ2: 0.88 / D res high: 3.82 Å / D res low: 50 Å / Num. obs: 14153 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
8.225010.0440.3975.2
6.538.2210.0920.9515.5
5.76.5310.1371.0855.6
5.185.710.1470.9535.7
4.815.1810.1570.9025.7
4.534.8110.1910.9355.8
4.34.5310.2440.9275.8
4.114.310.3760.9115.8
3.964.1110.6140.8925.8
3.823.9610.870.8935.8
ReflectionResolution: 3.82→50 Å / Num. obs: 14153 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.31 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Χ2: 0.885 / Net I/av σ(I): 13.222 / Net I/σ(I): 6.9 / Num. measured all: 80080
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.82-3.965.80.8713780.6880.3970.9580.89399.9
3.96-4.115.80.61413800.8310.2810.6770.892100
4.11-4.35.80.37613810.9030.1710.4140.911100
4.3-4.535.80.24413930.9570.1110.2680.92799.9
4.53-4.815.80.19113910.9660.0870.210.93599.9
4.81-5.185.70.15713930.9770.0720.1730.902100
5.18-5.75.70.14714190.9790.0680.1620.953100
5.7-6.535.60.13714210.9750.0640.1521.085100
6.53-8.225.50.09214560.9890.0430.1020.95199.9
8.22-505.20.04415410.9960.0210.0490.39799.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QRV, 3A1A

2qrv

3a1a


Resolution: 3.821→42.005 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 1392 9.9 %Random selection
Rwork0.224 18524 --
obs0.2285 13977 79.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 431.61 Å2 / Biso mean: 78.3298 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3.821→42.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5043 0 29 0 5072
Biso mean--59.01 --
Num. residues----623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065218
X-RAY DIFFRACTIONf_angle_d0.9777072
X-RAY DIFFRACTIONf_chiral_restr0.036744
X-RAY DIFFRACTIONf_plane_restr0.005916
X-RAY DIFFRACTIONf_dihedral_angle_d14.2431944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8211-3.90990.3406650.324872078545
3.9099-4.00760.31831020.316780290452
4.0076-4.11590.3499920.300981790953
4.1159-4.23690.3589960.274882992553
4.2369-4.37350.2981990.258981791654
4.3735-4.52960.3362980.247188598356
4.5296-4.71080.29271600.22531224138480
4.7108-4.92490.22291670.20011498166597
4.9249-5.18410.24311510.19391554170599
5.1841-5.50820.26971690.19615611730100
5.5082-5.93240.25091850.191815511736100
5.9324-6.52740.24111680.208215621730100
6.5274-7.46740.24771360.216915971733100
7.4674-9.39070.22531770.205115671744100
9.3907-42.00770.24121710.20321540171199

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