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- PDB-5nr3: Human DNMT3B PWWP domain in complex with ethambutol -

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Basic information

Entry
Database: PDB / ID: 5nr3
TitleHuman DNMT3B PWWP domain in complex with ethambutol
ComponentsDNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE / DNMT3B PWWP DOMAIN / HISTONE BINDING / BETA BARREL / LIGAND
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / : / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / : / catalytic complex / DNA methylation / PRC2 methylates histones and DNA ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / : / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / : / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression / transcription corepressor activity / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site ...PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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 / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ethambutol / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRondelet, G. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
F.R.S._FNRS_Televie7.4.532.15.F. Belgium
CitationJournal: To be published
Title: Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors
Authors: Rondelet, G. / Dal Maso, T. / Maniquet, A. / Themans, Q. / Wouters, J.
History
DepositionApr 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,0947
Polymers33,3982
Non-polymers6975
Water3,081171
1
A: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1915
Polymers16,6991
Non-polymers4924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9032
Polymers16,6991
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.200, 74.200, 155.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3B / Dnmt3b / DNA methyltransferase HsaIIIB / M.HsaIIIB


Mass: 16698.844 Da / Num. of mol.: 2 / Fragment: UNP residues 218-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-95E / Ethambutol / Ethambutol


Mass: 204.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H24N2O2 / Comment: medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 3.71 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350 / PH range: 5.7-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2015 / Details: X-RAY FLUORESCCENCE DETECTOR
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL-CUT SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→40.391 Å / Num. obs: 22766 / % possible obs: 99.7 % / Redundancy: 9.6 % / Biso Wilson estimate: 40.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 27
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 3.87 / Num. unique obs: 3549 / CC1/2: 0.883 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QKJ

3qkj


Resolution: 2.3→40.391 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2379 1137 5 %
Rwork0.1961 --
obs0.1982 22761 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.12 Å2 / Biso mean: 35.93 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 2.3→40.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 43 171 2318
Biso mean--48.98 41.19 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082206
X-RAY DIFFRACTIONf_angle_d1.1252960
X-RAY DIFFRACTIONf_chiral_restr0.079290
X-RAY DIFFRACTIONf_plane_restr0.004362
X-RAY DIFFRACTIONf_dihedral_angle_d15.571794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3001-2.40480.30631400.243726452785
2.4048-2.53150.28931400.224826602800
2.5315-2.69010.29181400.210326712811
2.6901-2.89780.26681400.204326552795
2.8978-3.18930.27751410.20626862827
3.1893-3.65050.22571420.182226982840
3.6505-4.59820.20431450.165327452890
4.5982-40.39750.21591490.208228643013

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