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- PDB-5nv0: Human DNMT3B PWWP domain in complex with 4-(dipropylamino)butyron... -

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Basic information

Entry
Database: PDB / ID: 5nv0
TitleHuman DNMT3B PWWP domain in complex with 4-(dipropylamino)butyronitrile
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 / 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
4-(dipropylamino)butanenitrile / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 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
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.journal_abbrev / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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)34,59913
Polymers33,3982
Non-polymers1,20111
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-107 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.260, 74.260, 159.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-405-

SO4

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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
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-9AH / 4-(dipropylamino)butanenitrile


Mass: 168.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20N2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.79 Å3/Da / Density % sol: 67.56 %
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 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2015
RadiationMonochromator: channel cut monochromator crystal (Si(111)) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.399→40.916 Å / Num. obs: 20558 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 66.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Net I/σ(I): 31.99
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 3229 / CC1/2: 0.9 / % possible all: 99.5

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Processing

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

3qkj


Resolution: 2.399→40.916 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.53
RfactorNum. reflection% reflection
Rfree0.2435 1027 5 %
Rwork0.1944 --
obs0.1968 20539 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.86 Å2 / Biso mean: 51.39 Å2 / Biso min: 25.52 Å2
Refinement stepCycle: final / Resolution: 2.399→40.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 69 73 2270
Biso mean--61.69 48.73 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082250
X-RAY DIFFRACTIONf_angle_d1.2113022
X-RAY DIFFRACTIONf_chiral_restr0.079292
X-RAY DIFFRACTIONf_plane_restr0.006366
X-RAY DIFFRACTIONf_dihedral_angle_d14.909800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3988-2.52530.3321420.28822694283699
2.5253-2.68350.33551450.259927602905100
2.6835-2.89060.29451440.255827312875100
2.8906-3.18140.30171460.250727662912100
3.1814-3.64150.31951450.211927812926100
3.6415-4.5870.24031490.171428292978100
4.587-40.92170.17831560.165129513107100

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