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- PDB-6u90: Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA -

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Basic information

Entry
Database: PDB / ID: 6u90
TitleCrystal structure of DNMT3B(N779A)-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


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 CpNpG 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 CpNpG substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpN 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 / 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: 3.00081756367 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: To Be Published
Title: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
Authors: Gao, L.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Dec 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)130,96510
Polymers130,0126
Non-polymers9534
Water37821
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)191.506, 191.506, 49.597
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: 33143.391 Da / Num. of mol.: 2 / Mutation: N779A
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, 25 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 21 / 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: 4.04 Å3/Da / Density % sol: 69.54 %
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: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3→47.8765 Å / Num. obs: 40636 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 67.3761830965 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.52
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 4056 / CC1/2: 0.858

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Processing

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

5yx2


Resolution: 3.00081756367→47.8765 Å / SU ML: 0.486596651553 / Cross valid method: FREE R-VALUE / σ(F): 1.97481947278 / Phase error: 28.5011384388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258952836435 2001 4.93696183168 %
Rwork0.219453008919 38530 -
obs0.2213620728 40531 99.6214821187 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.9542643825 Å2
Refinement stepCycle: LAST / Resolution: 3.00081756367→47.8765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7504 1020 64 21 8609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002934378576488947
X-RAY DIFFRACTIONf_angle_d0.52223110194312380
X-RAY DIFFRACTIONf_chiral_restr0.03882716423911351
X-RAY DIFFRACTIONf_plane_restr0.0027193220331423
X-RAY DIFFRACTIONf_dihedral_angle_d25.43326041693277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.00081756367-3.07580.4058088999461430.3476536601162722X-RAY DIFFRACTION98.3184625944
3.0758-3.1590.3283106635141440.3042182171822724X-RAY DIFFRACTION99.3762993763
3.159-3.25190.3636529903341440.3045443426692747X-RAY DIFFRACTION99.7584541063
3.2519-3.35690.3567023546131400.2883488097712807X-RAY DIFFRACTION99.7630331754
3.3569-3.47680.3352824919991420.2701565146462757X-RAY DIFFRACTION99.8622115053
3.4768-3.6160.275217124771400.2581119105032735X-RAY DIFFRACTION99.9304831422
3.616-3.78050.2914999125221460.2701490669142752X-RAY DIFFRACTION99.4850669413
3.7805-3.97970.2536626401031440.2294599876082749X-RAY DIFFRACTION99.79303208
3.9797-4.22890.2567177371841430.2013052892932761X-RAY DIFFRACTION99.9655765921
4.2289-4.55520.1996209639321420.1718901727212775X-RAY DIFFRACTION99.8288843258
4.5552-5.01320.2227442361941470.1738189698532762X-RAY DIFFRACTION100
5.0132-5.73750.2399047363891440.1945551510612721X-RAY DIFFRACTION99.9302406697
5.7375-7.22470.2574652835721400.2014943208082779X-RAY DIFFRACTION99.8631542935
7.2247-47.87650.2023662382461420.1828598047512739X-RAY DIFFRACTION98.969426314

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