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- PDB-6u8w: Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA -

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Basic information

Entry
Database: PDB / ID: 6u8w
TitleCrystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA
Components
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • CpGpT DNA (25-MER)
KeywordsTransferase/DNA / DNMT3B / DNMT3L / DNA methylation / Methyltransferase / transferase-DNA complex / TRANSFERASE
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / 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 / placenta development / DNA methylation / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / stem cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / enzyme activator activity / 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 / Vaccinia Virus protein VP39 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / 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: 2.94891558608 Å
AuthorsGao, L. / Zhang, Z.M. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2020
Title: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms.
Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / ...Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / Bashtrykov, P. / Wade, P.A. / Wang, G.G. / Jeltsch, A. / Song, J.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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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
E: CpGpT DNA (25-MER)
F: CpGpT DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,79910
Polymers129,9826
Non-polymers8174
Water19811
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)193.506, 193.506, 49.869
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31

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Components

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DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules ADBC

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


Mass: 33128.312 Da / Num. of mol.: 2 / Mutation: K777A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli) / Variant (production host): DE3
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 24163.705 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) / Variant (production host): DE3 / References: UniProt: Q9UJW3

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain CpGpT DNA (25-MER)


Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 15 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.94891558608→48.38 Å / Num. obs: 43944 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 76.8711214453 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.91
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 4333 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YX2

5yx2


Resolution: 2.94891558608→48.3765 Å / SU ML: 0.458235129573 / Cross valid method: FREE R-VALUE / σ(F): 1.96341412436 / Phase error: 27.4313585176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236316819954 1977 4.50783227307 %
Rwork0.215787357675 41880 -
obs0.216714672433 43857 99.6500874781 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.2882784718 Å2
Refinement stepCycle: LAST / Resolution: 2.94891558608→48.3765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7324 1020 54 11 8409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003567402804228752
X-RAY DIFFRACTIONf_angle_d0.68541036679112130
X-RAY DIFFRACTIONf_chiral_restr0.04231267462981325
X-RAY DIFFRACTIONf_plane_restr0.004776528082521393
X-RAY DIFFRACTIONf_dihedral_angle_d24.23494479843175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94891558608-3.02260.4399747057911420.3911535008742984X-RAY DIFFRACTION98.8302244704
3.0226-3.10440.3617157761081380.3156227218842967X-RAY DIFFRACTION99.36
3.1044-3.19570.3145492611991420.2959209495552976X-RAY DIFFRACTION99.5530012771
3.1957-3.29880.3268741623971400.2869722157073010X-RAY DIFFRACTION99.652008858
3.2988-3.41670.2815350260421340.2660879951082930X-RAY DIFFRACTION99.5775105622
3.4167-3.55350.3147372838691480.2648091431683047X-RAY DIFFRACTION99.8749609253
3.5535-3.71510.228161539291400.2403046015982994X-RAY DIFFRACTION99.9043672298
3.7151-3.91090.2234192723491340.2140174153022997X-RAY DIFFRACTION99.8724082935
3.9109-4.15580.2212024954551520.2091729575183014X-RAY DIFFRACTION99.8738170347
4.1558-4.47650.1900490861331400.173814112452981X-RAY DIFFRACTION99.6169805298
4.4765-4.92660.182591369341460.1841906625113001X-RAY DIFFRACTION100
4.9266-5.63850.2289129325081460.187297471322985X-RAY DIFFRACTION99.8405612245
5.6385-7.10030.2110272163431330.2080294741813019X-RAY DIFFRACTION99.9365884591
7.1003-48.37650.2274248836981420.1849810992212975X-RAY DIFFRACTION99.3307839388

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