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- PDB-5nvo: Human DNMT3B PWWP domain in complex with choline -

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Basic information

Entry
Database: PDB / ID: 5nvo
TitleHuman DNMT3B PWWP domain in complex with choline
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 / zinc ion binding / nucleoplasm / nucleus
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
CHOLINE ION / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 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)34,47113
Polymers33,3982
Non-polymers1,07311
Water1,26170
1
A: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3798
Polymers16,6991
Non-polymers6817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0915
Polymers16,6991
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.270, 74.270, 158.200
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-404-

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-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO
#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.: 70 / 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: 67.39 %
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: Feb 26, 2016
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: 2.4→40.78 Å / Num. obs: 20415 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 63.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 30.82
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 3197 / CC1/2: 0.7 / % possible all: 99.5

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Processing

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

3qkj


Resolution: 2.4→40.78 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.29
RfactorNum. reflection% reflection
Rfree0.244 1021 5 %
Rwork0.2066 --
obs0.2084 20409 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.92 Å2 / Biso mean: 57.21 Å2 / Biso min: 32.08 Å2
Refinement stepCycle: final / Resolution: 2.4→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 59 70 2189
Biso mean--70.29 55.83 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072172
X-RAY DIFFRACTIONf_angle_d1.1262924
X-RAY DIFFRACTIONf_chiral_restr0.076280
X-RAY DIFFRACTIONf_plane_restr0.006354
X-RAY DIFFRACTIONf_dihedral_angle_d13.943764
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 (%)
2.4002-2.52670.35391410.29892687282899
2.5267-2.6850.30221440.259327342878100
2.685-2.89220.2781430.246627142857100
2.8922-3.18320.29551450.243227572902100
3.1832-3.64360.26611460.202727642910100
3.6436-4.58950.19991470.175427992946100
4.5895-40.78560.22761550.199529333088100

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