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- PDB-8tdr: Crystal structure of the methyltransferase domain of DNMT3A homot... -

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Basic information

Entry
Database: PDB / ID: 8tdr
TitleCrystal structure of the methyltransferase domain of DNMT3A homotetramer
ComponentsDNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5)-methyltransferase 3A
KeywordsTRANSFERASE / DNA Methyltransferase
Function / homology
Function and homology information


: / positive regulation of cellular response to hypoxia / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity ...: / positive regulation of cellular response to hypoxia / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / XY body / DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / cellular response to ethanol / response to vitamin A / : / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / response to cocaine / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to amino acid stimulus / response to lead ion / euchromatin / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / transcription corepressor activity / response to estradiol / cellular response to hypoxia / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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. ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsLu, J.W. / Song, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal structure of the homo-tetrameric DNMT3A methyltransferase domain
Authors: Lu, J.W. / Song, J.K.
History
DepositionJul 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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 3A
C: DNA (cytosine-5)-methyltransferase 3A
E: DNA (cytosine-5)-methyltransferase 3A
H: DNA (cytosine-5)-methyltransferase 3A
F: DNA (cytosine-5)-methyltransferase 3A
D: DNA (cytosine-5)-methyltransferase 3A
G: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,41612
Polymers262,8798
Non-polymers1,5384
Water0
1
A: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3A
E: DNA (cytosine-5)-methyltransferase 3A
F: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2086
Polymers131,4394
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (cytosine-5)-methyltransferase 3A
H: DNA (cytosine-5)-methyltransferase 3A
D: DNA (cytosine-5)-methyltransferase 3A
G: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2086
Polymers131,4394
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.429, 179.429, 108.065
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
DNA (cytosine-5)-methyltransferase 3A / DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / Cysteine methyltransferase DNMT3A / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA


Mass: 32859.844 Da / Num. of mol.: 8 / Fragment: methyltransferase domain (UNP residues 628-912)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2-0.4 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.32→50 Å / Num. obs: 57297 / % possible obs: 100 % / Redundancy: 3.9 % / Biso Wilson estimate: 84.77 Å2 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.127 / Rrim(I) all: 0.254 / Χ2: 0.583 / Net I/σ(I): 3.3 / Num. measured all: 225061
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.32-3.443.71.31956890.8340.7821.5380.53100
3.44-3.583.70.95257250.710.5741.1160.54199.9
3.58-3.743.80.70858160.6220.4150.8230.59100
3.74-3.944.10.58656640.7560.3280.6740.572100
3.94-4.1840.41857360.8810.2350.4810.545100
4.18-4.513.90.24357480.9460.1380.2810.607100
4.51-4.963.80.17557120.970.1030.2030.591100
4.96-5.674.20.16357530.9790.090.1860.55100
5.67-7.153.90.13157320.9810.0760.1520.57100
7.15-504.10.04257220.9980.0240.0490.72699.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5YX2

5yx2


Resolution: 3.32→46.29 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 2003 3.51 %
Rwork0.2097 55056 -
obs0.2108 57059 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.69 Å2 / Biso mean: 81.129 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.32→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14251 0 104 0 14355
Biso mean--75.66 --
Num. residues----1820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.32-3.40.29841450.31963823396898
3.4-3.50.36211380.30473950408899
3.5-3.60.30051480.2743967411599
3.6-3.720.29311380.25239054043100
3.72-3.850.2581400.242739424082100
3.85-40.23611380.2439594097100
4-4.180.26521480.206839614109100
4.18-4.40.23841410.194939114052100
4.41-4.680.24611400.175839684108100
4.68-5.040.20041390.177139294068100
5.04-5.550.22581520.189639394091100
5.55-6.350.20811440.207439714115100
6.35-7.990.20011420.196939374079100
7.99-46.290.21251500.17383894404498
Refinement TLS params.Method: refined / Origin x: 36.4286 Å / Origin y: -51.9343 Å / Origin z: 34.8961 Å
111213212223313233
T0.547 Å20.0057 Å2-0.0059 Å2-0.3904 Å20.0688 Å2--0.398 Å2
L-0.0197 °2-0.0179 °20.0134 °2-0.118 °2-0.1772 °2--0.0264 °2
S0.0281 Å °0.0067 Å °-0.0058 Å °-0.0053 Å °-0.04 Å °-0.0463 Å °0.0011 Å °0.211 Å °0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA626 - 1005
2X-RAY DIFFRACTION1allB626 - 1005
3X-RAY DIFFRACTION1allC626 - 1005
4X-RAY DIFFRACTION1allE629 - 912
5X-RAY DIFFRACTION1allH628 - 912
6X-RAY DIFFRACTION1allF628 - 912
7X-RAY DIFFRACTION1allD626 - 1005
8X-RAY DIFFRACTION1allG629 - 912

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