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- PDB-8te4: Crystal structure of the methyltransferase domain of R882H/N879A ... -

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Basic information

Entry
Database: PDB / ID: 8te4
TitleCrystal structure of the methyltransferase domain of R882H/N879A 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 / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins ...positive regulation of cellular response to hypoxia / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / XY body / cellular response to ethanol / response to vitamin A / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / PRC2 methylates histones and DNA / response to cocaine / 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 / methylation / 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 / DNMT3, cysteine rich ADD domain, GATA1-like 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. ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like 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 / 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: 2.65 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 methyltransferase domain of R882H/N879A DNMT3A homotetramer
Authors: Lu, J.W. / Song, J.K.
History
DepositionJul 5, 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)265,39328
Polymers262,3828
Non-polymers3,01120
Water10,953608
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)132,88116
Polymers131,1914
Non-polymers1,69012
Water724
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)132,51212
Polymers131,1914
Non-polymers1,3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.068, 178.068, 109.909
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: 32797.770 Da / Num. of mol.: 8 / Fragment: methyltransferase domain (UNP residues 628-912) / Mutation: R882H,N879A
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
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: 3.83 Å3/Da / Density % sol: 67.92 %
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: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 113612 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 53.14 Å2 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.073 / Rrim(I) all: 0.172 / Χ2: 1.234 / Net I/σ(I): 7 / Num. measured all: 621954
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.65-2.745.31.562113480.3450.751.7341.036
2.74-2.855.41.168113370.4790.5581.2961.058
2.85-2.985.30.833114150.6420.3980.9241.113
2.98-3.145.40.549113200.8250.2620.6081.165
3.14-3.345.40.361113700.9170.1710.41.25
3.34-3.65.50.211113460.9740.0990.2331.344
3.6-3.965.60.135113870.9870.0630.1491.376
3.96-4.535.60.099113460.9930.0460.1091.509
4.53-5.715.60.089113560.9930.0420.0991.371
5.71-505.70.038113870.9990.0170.0411.092

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Processing

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

5yx2


Resolution: 2.65→46.76 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 1995 1.77 %
Rwork0.2027 110935 -
obs0.2033 112930 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.97 Å2 / Biso mean: 58.7591 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.65→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13969 0 200 610 14779
Biso mean--66.68 52.77 -
Num. residues----1761
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 (%)
2.65-2.710.40551400.34537695783597
2.71-2.790.30231400.3187889802999
2.79-2.870.39151460.29617910805699
2.87-2.960.33061420.28627938808099
2.96-3.070.30791440.27577874801899
3.07-3.190.32331400.25437946808699
3.19-3.330.26261410.21779628103100
3.33-3.510.24611320.214479418073100
3.51-3.730.22781430.191179778120100
3.73-4.020.16911500.179479838133100
4.02-4.420.19291420.15779458087100
4.42-5.060.17681480.153679858133100
5.06-6.370.20141390.175779608099100
6.37-46.760.241480.18357930807899
Refinement TLS params.Method: refined / Origin x: 35.5363 Å / Origin y: -51.78 Å / Origin z: 35.6676 Å
111213212223313233
T0.5509 Å20.0024 Å2-0.0003 Å2-0.5165 Å20.1312 Å2--0.5709 Å2
L-0.1619 °2-0.0063 °20.0004 °2-0.3199 °2-0.295 °2--0.1708 °2
S0.0172 Å °0.0032 Å °-0.0014 Å °-0.0022 Å °-0.1288 Å °-0.2183 Å °0.0023 Å °0.2223 Å °0.1012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA626 - 1701
2X-RAY DIFFRACTION1allB626 - 1701
3X-RAY DIFFRACTION1allB1801
4X-RAY DIFFRACTION1allC626 - 1001
5X-RAY DIFFRACTION1allC1201 - 1501
6X-RAY DIFFRACTION1allE628 - 912
7X-RAY DIFFRACTION1allH628 - 912
8X-RAY DIFFRACTION1allF628 - 912
9X-RAY DIFFRACTION1allD626 - 1005
10X-RAY DIFFRACTION1allD1101 - 1401
11X-RAY DIFFRACTION1allG629 - 912
12X-RAY DIFFRACTION1allS1 - 642

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