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- PDB-8xee: Human DNMT3B mutant-R823G -

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Basic information

Entry
Database: PDB / ID: 8xee
TitleHuman DNMT3B mutant-R823G
Components
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3B
KeywordsDNA BINDING PROTEIN / Methyltransferase / DNA methylation
Function / homology
Function and homology information


epigenetic programing of female pronucleus / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates ...epigenetic programing of female pronucleus / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / autosome genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / DNA methylation / enzyme activator activity / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / placenta development / NoRC negatively regulates rRNA expression / transcription corepressor activity / spermatogenesis / methylation / negative regulation of DNA-templated transcription / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / 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. ...DNA (cytosine-5)-methyltransferase 3B, ADD domain / 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 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3B / DNA (cytosine-5)-methyltransferase 3-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsCho, C.-C. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Protein Sci. / Year: 2024
Title: Molecular mechanisms for DNA methylation defects induced by ICF syndrome-linked mutations in DNMT3B.
Authors: Cho, C.C. / Fei, C.Y. / Jiang, B.C. / Yang, W.Z. / Yuan, H.S.
History
DepositionDec 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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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 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8646
Polymers112,0954
Non-polymers7692
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.107, 194.107, 49.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 32420.523 Da / Num. of mol.: 2 / Mutation: R823G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 23627.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJW3
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 4.82 Å3/Da / Density % sol: 74.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: HEPES (pH 7.5), MgCl2, 2-methyl-2,4-pentanediol, spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.03→30 Å / Num. obs: 40728 / % possible obs: 100 % / Redundancy: 5.2 % / CC1/2: 0.9713 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.03-3.144.60.48540650.9050.9750.2520.5481.215100
3.14-3.264.70.42740690.90.9730.220.4811.215100
3.26-3.414.70.27240680.9550.9880.140.3061.127100
3.41-3.594.90.17441030.9780.9940.0880.1961.086100
3.59-3.8250.12340880.9880.9970.0610.1371.067100
3.82-4.115.10.09840590.9940.9980.0480.1091.069100
4.11-4.525.40.06740940.9960.9990.0320.0741.066100
4.52-5.175.70.05240340.9980.9990.0240.0570.998100
5.17-6.515.90.04340850.99910.0190.0471.05100
6.51-305.80.0254063110.0110.0271.00399.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.03→26.92 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1984 4.88 %
Rwork0.2151 --
obs0.2161 40683 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.03→26.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7497 0 52 0 7549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027744
X-RAY DIFFRACTIONf_angle_d0.52910476
X-RAY DIFFRACTIONf_dihedral_angle_d12.9272905
X-RAY DIFFRACTIONf_chiral_restr0.0411128
X-RAY DIFFRACTIONf_plane_restr0.0041331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.10.37511480.30292765X-RAY DIFFRACTION100
3.1-3.190.3141480.28432734X-RAY DIFFRACTION100
3.19-3.280.2711460.27522788X-RAY DIFFRACTION100
3.28-3.390.2911360.26512729X-RAY DIFFRACTION100
3.39-3.510.28291360.24922817X-RAY DIFFRACTION100
3.51-3.650.25311460.22772730X-RAY DIFFRACTION100
3.65-3.810.24421500.21362801X-RAY DIFFRACTION100
3.81-4.010.2361470.23642730X-RAY DIFFRACTION100
4.02-4.270.26361350.20452756X-RAY DIFFRACTION100
4.27-4.590.19351340.18842778X-RAY DIFFRACTION100
4.59-5.050.2211340.19512785X-RAY DIFFRACTION100
5.05-5.780.23241400.20822754X-RAY DIFFRACTION100
5.79-7.250.21121380.21032788X-RAY DIFFRACTION100
7.26-26.920.18561460.17572744X-RAY DIFFRACTION99

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