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- PDB-5ciu: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain -

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Basic information

Entry
Database: PDB / ID: 5ciu
TitleStructural basis of the recognition of H3K36me3 by DNMT3B PWWP domain
Components
  • DNA (cytosine-5)-methyltransferase 3B
  • Histone H3.2
KeywordsTRANSFERASE / PROTEIN-PEPTIDE COMPLEX / DNMT3B / PWWP DOMAIN / HISTONE BINDING / H3K36ME3 / METHYLTRANSFERASE 3 BETA / S-ADENOSYL-L-METHIONINE / ZINC-FINGER
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 / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening ...: / 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 / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / 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 / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein heterodimerization activity / Amyloid fiber formation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / 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 / 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 / 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 / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Histone-fold / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Histone H3.2 / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å
AuthorsRondelet, G. / DAL MASO, T. / Willems, L. / Wouters, J.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B.
Authors: Rondelet, G. / Dal Maso, T. / Willems, L. / Wouters, J.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 2.0Jun 12, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / database_PDB_rev / database_PDB_rev_record / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.occupancy / _audit_author.name
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
C: Histone H3.2
D: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8345
Polymers36,7424
Non-polymers921
Water2,936163
1
A: DNA (cytosine-5)-methyltransferase 3B
D: Histone H3.2


Theoretical massNumber of molelcules
Total (without water)18,3712
Polymers18,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-9 kcal/mol
Surface area7750 Å2
MethodPISA
2
B: DNA (cytosine-5)-methyltransferase 3B
C: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4633
Polymers18,3712
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.437, 73.437, 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
11A-416-

HOH

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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: Protein/peptide Histone H3.2 / Histone H3/m / Histone H3/o


Mass: 1671.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M SODIUM CITRATE TRIBASIC

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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: Jun 27, 2014 / 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: 2.24→50 Å / Num. obs: 24436 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 49.9 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Χ2: 1.042 / Net I/σ(I): 18.44 / Num. measured all: 168485
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.24-2.370.8460.6332.9526884387238160.68398.6
2.37-2.540.9470.3815.0926368366436640.411100
2.54-2.740.9810.2079.2724296338633860.224100
2.74-30.9950.11615.7122510315731560.125100
3-3.350.9970.0724.5120093288128800.075100
3.35-3.860.9980.0513317037254225410.055100
3.86-4.720.9980.04537.1314269217421730.048100
4.72-6.610.9990.03937.811104173417310.04399.8
6.610.9990.03237.58592410619980.03594.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.22 Å40.59 Å
Translation5.22 Å40.59 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QKJ

3qkj


Resolution: 2.24→36.718 Å / FOM work R set: 0.787 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1905 7.8 %Random selection
Rwork0.2241 22531 --
obs0.2268 24436 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.99 Å2 / Biso mean: 46.45 Å2 / Biso min: 21.11 Å2
Refinement stepCycle: final / Resolution: 2.24→36.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 6 163 2266
Biso mean--55.14 49.3 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092162
X-RAY DIFFRACTIONf_angle_d1.2042898
X-RAY DIFFRACTIONf_chiral_restr0.087282
X-RAY DIFFRACTIONf_plane_restr0.005354
X-RAY DIFFRACTIONf_dihedral_angle_d13.937774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.24-2.2960.38151360.316816041740100
2.296-2.35810.35331330.299215681701100
2.3581-2.42750.31451340.278815801714100
2.4275-2.50580.34551360.288515821718100
2.5058-2.59540.32661340.273615841718100
2.5954-2.69920.31851350.260915961731100
2.6992-2.8220.34341400.256416121752100
2.822-2.97080.31841350.248115711706100
2.9708-3.15680.31661320.246516061738100
3.1568-3.40040.28061320.225316161748100
3.4004-3.74230.25011360.197816331769100
3.7423-4.28310.18511330.190416321765100
4.2831-5.39350.20141410.183616531794100
5.3935-36.72340.24721480.23471694184297

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