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- PDB-6u8x: Crystal structure of DNMT3B-DNMT3L in complex with CpApG DNA -

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Basic information

Entry
Database: PDB / ID: 6u8x
TitleCrystal structure of DNMT3B-DNMT3L in complex with CpApG DNA
Components
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • CpApG DNA (25-MER)
KeywordsTransferase/DNA / DNMT3B / DNMT3L / DNA methylation / Methyltransferase / transferase-DNA complex / TRANSFERASE
Function / homology
Function and homology information


epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity ...epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / ESC/E(Z) complex / SUMOylation of DNA methylation proteins / 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 / stem cell differentiation / condensed nuclear chromosome / post-embryonic development / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / cytoplasm / cytosol
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. ...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: 2.95063876297 Å
AuthorsGao, L. / 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: CpApG DNA (25-MER)
F: CpApG DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,91610
Polymers130,0986
Non-polymers8174
Water34219
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)193.845, 193.845, 49.884
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: 33186.414 Da / Num. of mol.: 2
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 CpApG 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, 23 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.28 Å3/Da / Density % sol: 71.29 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl (pH 8.0), 100 mM MgCl2, 7% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.95→42.8826289855 Å / Num. obs: 43984 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 72.2981583492 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 2.95→3.06 Å / Num. unique obs: 4359 / CC1/2: 0.763

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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: 2.95063876297→42.8826289855 Å / SU ML: 0.490640577389 / Cross valid method: FREE R-VALUE / σ(F): 1.9633455681 / Phase error: 28.4198116328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251508134801 1995 4.54245315239 %
Rwork0.22720181358 41924 -
obs0.228294539359 43919 99.6392758292 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.2683597198 Å2
Refinement stepCycle: LAST / Resolution: 2.95063876297→42.8826289855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7487 1022 54 19 8582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002995133372968914
X-RAY DIFFRACTIONf_angle_d0.62093983447812332
X-RAY DIFFRACTIONf_chiral_restr0.04153467436251343
X-RAY DIFFRACTIONf_plane_restr0.004088590810441413
X-RAY DIFFRACTIONf_dihedral_angle_d23.90933612733284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95063876297-3.02440.4070705299651440.3781164728342929X-RAY DIFFRACTION98.8420714056
3.0244-3.10620.3263755684411540.3123100522053019X-RAY DIFFRACTION99.2182614134
3.1062-3.19750.3049883759681420.2880711768142944X-RAY DIFFRACTION99.5805098419
3.1975-3.30070.3270227784551440.2866085921793036X-RAY DIFFRACTION99.9057492931
3.3007-3.41860.2733211241021340.2542495788932964X-RAY DIFFRACTION99.5181496948
3.4186-3.55540.2945110845791520.2638625064323039X-RAY DIFFRACTION99.8123240538
3.5554-3.71720.275106502031480.2493337970272973X-RAY DIFFRACTION99.9359590138
3.7172-3.9130.2919073653631310.2333413441712994X-RAY DIFFRACTION99.3009215126
3.913-4.1580.2508972832291420.2254788043113038X-RAY DIFFRACTION99.9057492931
4.158-4.47870.205131478091360.1932375758842975X-RAY DIFFRACTION99.8715890851
4.4787-4.92880.2435627712971400.1992434732783017X-RAY DIFFRACTION100
4.9288-5.64070.2432104252431430.21183943523011X-RAY DIFFRACTION99.9366286439
5.6407-7.10140.2412896443911440.2142959795363006X-RAY DIFFRACTION99.8731769182
7.1014-42.88262898550.1978684340041410.1936568806812979X-RAY DIFFRACTION99.2682150811

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