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- PDB-6f57: Crystal structure of DNMT3A-DNMT3L in complex with single CpG-con... -

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Basic information

Entry
Database: PDB / ID: 6f57
TitleCrystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA
Components
  • DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')
  • DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3A
Keywordstransferase/DNA / DNMT3A / DNMT3L / DNA methylation / DNA binding protein / transferase-DNA complex
Function / homology
Function and homology information


epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / cellular response to bisphenol A ...epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / XY body / response to vitamin A / DNA methylation-dependent constitutive heterochromatin formation / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / hepatocyte apoptotic process / lncRNA binding / negative regulation of gene expression, epigenetic / male meiosis I / cellular response to ethanol / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / placenta development / DNA methylation / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / response to cocaine / stem cell differentiation / cellular response to amino acid stimulus / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / enzyme activator activity / euchromatin / response to lead ion / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / neuron differentiation / transcription corepressor activity / response to estradiol / spermatogenesis / methylation / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / 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 ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / 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 3-like / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.098 Å
AuthorsZhang, Z.M. / Song, J.
CitationJournal: Nature / Year: 2018
Title: Structural basis for DNMT3A-mediated de novo DNA methylation.
Authors: Zhang, Z.M. / Lu, R. / Wang, P. / Yu, Y. / Chen, D. / Gao, L. / Liu, S. / Ji, D. / Rothbart, S.B. / Wang, Y. / Wang, G.G. / Song, J.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _refine_hist.d_res_low
Revision 2.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
E: DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')
F: DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')
G: DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')
H: DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,25610
Polymers126,4878
Non-polymers7692
Water00
1
A: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3-like
E: DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')
F: DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6285
Polymers63,2444
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-16 kcal/mol
Surface area21590 Å2
MethodPISA
2
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
G: DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')
H: DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6285
Polymers63,2444
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-15 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.611, 49.559, 162.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase HsaIIIA / M.HsaIIIA


Mass: 32715.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y6K1, 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 BL21(DE3) (bacteria) / References: UniProt: Q9UJW3
#3: DNA chain DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')


Mass: 3094.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')


Mass: 3270.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 7% PEG4000, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2, 166 mM imidazole (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.09→47.72 Å / Num. obs: 26661 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 9.1
Reflection shellResolution: 3.09→3.2 Å / Rmerge(I) obs: 0.982

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QRV

2qrv


Resolution: 3.098→47.72 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 2020 7.58 %
Rwork0.211 --
obs0.2133 26650 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.098→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 805 52 0 7613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057899
X-RAY DIFFRACTIONf_angle_d0.77610895
X-RAY DIFFRACTIONf_dihedral_angle_d17.6882864
X-RAY DIFFRACTIONf_chiral_restr0.031193
X-RAY DIFFRACTIONf_plane_restr0.0031267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0976-3.1750.36571410.33671619X-RAY DIFFRACTION96
3.175-3.26090.30241370.31171723X-RAY DIFFRACTION99
3.2609-3.35680.30281480.27731721X-RAY DIFFRACTION99
3.3568-3.46510.34721440.26651725X-RAY DIFFRACTION99
3.4651-3.58890.27341280.24151752X-RAY DIFFRACTION99
3.5889-3.73260.26941500.22091712X-RAY DIFFRACTION99
3.7326-3.90240.19841470.20021737X-RAY DIFFRACTION99
3.9024-4.1080.19811410.19611774X-RAY DIFFRACTION100
4.108-4.36520.20421410.171751X-RAY DIFFRACTION100
4.3652-4.7020.20351400.1711779X-RAY DIFFRACTION100
4.702-5.17460.20861510.1811765X-RAY DIFFRACTION100
5.1746-5.92220.22491410.20211809X-RAY DIFFRACTION100
5.9222-7.45680.27541540.21111818X-RAY DIFFRACTION100
7.4568-47.72160.22291570.1881945X-RAY DIFFRACTION100

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