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- PDB-4qbs: Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3... -

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Basic information

Entry
Database: PDB / ID: 4qbs
TitleCrystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide
Components
  • DNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5)-methyltransferase 3A
  • Histone H3
KeywordsTRANSFERASE / Zinc Finger / Histone Binding
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / cellular response to amino acid stimulus / response to lead ion / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / neuron differentiation / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / response to toxic substance / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / response to estradiol / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / methylation / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H3.1 / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, H. / Li, H.
CitationJournal: To be Published
Title: Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs
Authors: Noh, K. / Wang, H. / Kim, H. / Wenderski, W. / Fang, F. / Li, C. / Dewell, S. / Wu, X. / Ferris, A. / Hughes, S.H. / Zheng, D. / Melnick, A.M. / Patel, D.J. / Li, H. / Allis, C.D.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3A
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8546
Polymers16,5622
Non-polymers2924
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-3 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.286, 57.286, 71.923
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 15705.123 Da / Num. of mol.: 1 / Fragment: ADD Domain, UNP residues 456-661 / Mutation: E545R
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/peptide Histone H3 /


Mass: 856.861 Da / Num. of mol.: 1 / Fragment: H3 N-terminal 1-10 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE ENTITY2 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE ...THE SEQUENCE OF THE ENTITY2 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.1M Bis-Tris, 0.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 13016 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rsym value: 0.091
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.8-1.831100
1.83-1.861100
1.86-1.91100
1.9-1.941100
1.94-1.981100
1.98-2.031100
2.03-2.081100
2.08-2.131100
2.13-2.21100
2.2-2.271100
2.27-2.351100
2.35-2.44199.7
2.44-2.55199.7
2.55-2.69199.7
2.69-2.86199.8
2.86-3.08199.2
3.08-3.39199.3
3.39-3.88198.2
3.88-4.88197.9
4.88-50194.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.838 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 636 4.89 %RANDOM
Rwork0.1667 ---
obs0.1685 13009 99.43 %-
all-13083 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 8 125 1274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011182
X-RAY DIFFRACTIONf_angle_d1.3081599
X-RAY DIFFRACTIONf_dihedral_angle_d14.456446
X-RAY DIFFRACTIONf_chiral_restr0.053166
X-RAY DIFFRACTIONf_plane_restr0.006211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.93890.23381390.18432396100
1.9389-2.1340.22871380.17412448100
2.134-2.44280.25351060.17062473100
2.4428-3.07750.20541300.17892489100
3.0775-40.84860.17271230.1545256798

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