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- PDB-6r3e: Human DNMT3B PWWP domain in complex with triisopropanolamine -

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Basic information

Entry
Database: PDB / ID: 6r3e
TitleHuman DNMT3B PWWP domain in complex with triisopropanolamine
ComponentsDNA (cytosine-5)-methyltransferase 3B,DNA (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 / Defective pyroptosis / NoRC negatively regulates rRNA expression ...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 / methylation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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 ...PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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 / 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
Triisopropanolamine / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.269 Å
AuthorsRondelet, G. / Dal Maso, T. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Other government7.4.532.15.F. Belgium
CitationJournal: To be published
Title: Targeting PWWP domain of DNMT3B for epigenetic cancer therapy: identification and structural characterization of potential protein-protein interaction inhibitors
Authors: Rondelet, G. / Dal Maso, T. / Maniquet, A. / Themans, Q. / Wouters, J.
History
DepositionMar 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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,DNA (cytosine-5)-methyltransferase 3B
B: DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3348
Polymers61,6632
Non-polymers6726
Water2,072115
1
A: DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3115
Polymers30,8311
Non-polymers4794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0233
Polymers30,8311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.257, 74.257, 158.187
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-644-

HOH

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Components

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


Mass: 30831.361 Da / Num. of mol.: 2
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-96H / Triisopropanolamine


Mass: 191.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H21NO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.77 Å3/Da / Density % sol: 67.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, 0.2 M Li2SO4, 23-33% PEG3350 / PH range: 5.7-6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2014
RadiationMonochromator: channel cut monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.269→40.776 Å / Num. obs: 45066 / % possible obs: 99.91 % / Redundancy: 12.6 % / Biso Wilson estimate: 61.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Net I/σ(I): 37.74
Reflection shellResolution: 2.269→2.41 Å / Num. unique obs: 24064

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QKJ

3qkj


Resolution: 2.269→40.775 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 3696 8.2 %
Rwork0.2176 --
obs0.2214 45066 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.269→40.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 38 115 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082212
X-RAY DIFFRACTIONf_angle_d1.0012975
X-RAY DIFFRACTIONf_dihedral_angle_d3.5051255
X-RAY DIFFRACTIONf_chiral_restr0.05291
X-RAY DIFFRACTIONf_plane_restr0.006364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2694-2.29930.43641330.45671566X-RAY DIFFRACTION97
2.2993-2.33080.45411440.41941592X-RAY DIFFRACTION100
2.3308-2.36410.38921440.38321554X-RAY DIFFRACTION100
2.3641-2.39940.37971520.37271632X-RAY DIFFRACTION100
2.3994-2.43690.35671420.35331550X-RAY DIFFRACTION100
2.4369-2.47680.35851520.34341625X-RAY DIFFRACTION100
2.4768-2.51950.31421380.30771557X-RAY DIFFRACTION100
2.5195-2.56530.3411480.29771612X-RAY DIFFRACTION100
2.5653-2.61460.32181420.2831573X-RAY DIFFRACTION100
2.6146-2.6680.36241440.27991579X-RAY DIFFRACTION100
2.668-2.7260.30681440.26071615X-RAY DIFFRACTION100
2.726-2.78940.37521420.2681555X-RAY DIFFRACTION100
2.7894-2.85910.26791320.24561671X-RAY DIFFRACTION100
2.8591-2.93640.28611380.24341572X-RAY DIFFRACTION100
2.9364-3.02280.23511460.22991566X-RAY DIFFRACTION100
3.0228-3.12030.30811360.24381628X-RAY DIFFRACTION100
3.1203-3.23180.27071540.2251607X-RAY DIFFRACTION100
3.2318-3.36120.31741380.2351573X-RAY DIFFRACTION100
3.3612-3.51410.30811440.21811593X-RAY DIFFRACTION100
3.5141-3.69920.23351290.21871606X-RAY DIFFRACTION100
3.6992-3.93080.2331380.20031588X-RAY DIFFRACTION100
3.9308-4.2340.21881420.18461558X-RAY DIFFRACTION100
4.234-4.65950.23621500.17551621X-RAY DIFFRACTION100
4.6595-5.33250.2211410.17021596X-RAY DIFFRACTION100
5.3325-6.71360.23371440.19971587X-RAY DIFFRACTION100
6.7136-40.78140.25511390.19251594X-RAY DIFFRACTION100

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