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- PDB-3svm: Human MPP8 - human DNMT3AK47me2 peptide -

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Basic information

Entry
Database: PDB / ID: 3svm
TitleHuman MPP8 - human DNMT3AK47me2 peptide
Components
  • DNA (cytosine-5)-methyltransferase 3A
  • M-phase phosphoprotein 8
KeywordsTRANSFERASE / epigenetics / methyl-lysine binding / Chromodomain / The dimethylated human DNMT3AK47me2 is recognized by the chromodomain of MPP8 / MPP8 chromodomain / dimethylated lysine
Function / homology
Function and homology information


positive regulation of cellular response to hypoxia / positive regulation of DNA methylation-dependent heterochromatin formation / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / : / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity ...positive regulation of cellular response to hypoxia / positive regulation of DNA methylation-dependent heterochromatin formation / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / : / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / XY body / cellular response to ethanol / response to vitamin A / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / methylated histone binding / histone reader activity / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / cellular response to amino acid stimulus / response to lead ion / euchromatin / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / cilium / nuclear matrix / transcription corepressor activity / nucleosome / response to estradiol / cellular response to hypoxia / methylation / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / ADD domain / ADD domain profile. / Chromo domain, conserved site / Chromo domain signature. / DNA methylase, C-5 cytosine-specific, active site ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / ADD domain / ADD domain profile. / Chromo domain, conserved site / Chromo domain signature. / 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 / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
M-phase phosphoprotein 8 / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsChang, Y. / Horton, J.R. / Zhang, X. / Cheng, X.
CitationJournal: Nat Commun / Year: 2011
Title: MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a.
Authors: Chang, Y. / Sun, L. / Kokura, K. / Horton, J.R. / Fukuda, M. / Espejo, A. / Izumi, V. / Koomen, J.M. / Bedford, M.T. / Zhang, X. / Shinkai, Y. / Fang, J. / Cheng, X.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M-phase phosphoprotein 8
P: DNA (cytosine-5)-methyltransferase 3A


Theoretical massNumber of molelcules
Total (without water)9,0502
Polymers9,0502
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area5020 Å2
MethodPISA
2
A: M-phase phosphoprotein 8
P: DNA (cytosine-5)-methyltransferase 3A

A: M-phase phosphoprotein 8
P: DNA (cytosine-5)-methyltransferase 3A


Theoretical massNumber of molelcules
Total (without water)18,1014
Polymers18,1014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4110 Å2
ΔGint-24 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.090, 43.900, 90.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein M-phase phosphoprotein 8 / Two hybrid-associated protein 3 with RanBPM / Twa3


Mass: 7344.350 Da / Num. of mol.: 1 / Fragment: unp residues 55-116
Source method: isolated from a genetically manipulated source
Details: 6xHis-SUMO tag / Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Plasmid: pXC941 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99549
#2: Protein/peptide DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA


Mass: 1705.937 Da / Num. of mol.: 1 / Fragment: unp residues 40-53 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% polyethylene glycol 1500, 20% polyethylene glycol 400 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→30 Å / Num. obs: 3624 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.6
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.3 / % possible all: 82

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QO2

3qo2


Resolution: 2.31→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 184 -RANDOM
Rwork0.257 ---
obs0.257 3465 90.9 %-
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1--11.75 Å20 Å20 Å2
2--16.67 Å20 Å2
3----4.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.4 Å
Luzzati d res low-30 Å
Luzzati sigma a0.43 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.31→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms578 0 0 24 602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.31→2.45 Å / Rfactor Rfree error: 0.067
RfactorNum. reflection% reflection
Rfree0.368 22 -
Rwork0.316 --
obs--68.7 %

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