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- PDB-5yx2: Crystal structure of DNMT3A-DNMT3L in complex with DNA containing... -

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Basic information

Entry
Database: PDB / ID: 5yx2
TitleCrystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites
Components
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • DNA (25-MER)
KeywordsTRANSFERASE/TRANSFERASE REGULATOR/DNA / DNMT3A / DNMT3L / DNA methylation / TRANSFERASE-TRANSFERASE REGULATOR-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 / protein-cysteine methyltransferase activity / transposable element silencing by heterochromatin formation / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / unmethylated CpG binding ...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 / protein-cysteine methyltransferase activity / transposable element silencing by heterochromatin formation / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / unmethylated CpG binding / 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 / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / 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 / placenta development / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / condensed nuclear chromosome / PRC2 methylates histones and DNA / Defective pyroptosis / post-embryonic development / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / cellular response to amino acid stimulus / response to cocaine / enzyme activator activity / response to lead ion / euchromatin / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / neuron differentiation / transcription corepressor activity / response to estradiol / spermatogenesis / cellular response to hypoxia / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / cytosol / cytoplasm
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 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: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 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 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 22, 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

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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
D: DNA (cytosine-5)-methyltransferase 3A
C: DNA (cytosine-5)-methyltransferase 3-like
E: DNA (25-MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,25214
Polymers128,9306
Non-polymers1,3218
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15530 Å2
ΔGint-66 kcal/mol
Surface area44790 Å2
Unit cell
Length a, b, c (Å)205.424, 205.424, 89.337
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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

#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) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 24050.547 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) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJW3

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain DNA (25-MER)


Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 83 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / 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.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris-HCl (pH 7.0), 200 mM NaH2PO4, 5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 40049 / % possible obs: 98.5 % / Redundancy: 3.3 % / Net I/σ(I): 15.9
Reflection shellResolution: 2.65→2.74 Å

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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: 2.653→33.114 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2217 2005 5.01 %
Rwork0.1906 --
obs0.1922 40049 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.653→33.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7249 1020 36 75 8380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048618
X-RAY DIFFRACTIONf_angle_d0.73111914
X-RAY DIFFRACTIONf_dihedral_angle_d20.1323178
X-RAY DIFFRACTIONf_chiral_restr0.031301
X-RAY DIFFRACTIONf_plane_restr0.0041358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6528-2.71910.29111460.27212746X-RAY DIFFRACTION99
2.7191-2.79260.33071400.26792697X-RAY DIFFRACTION99
2.7926-2.87470.31051440.26682748X-RAY DIFFRACTION99
2.8747-2.96750.28111430.26342741X-RAY DIFFRACTION99
2.9675-3.07340.32791480.25052731X-RAY DIFFRACTION99
3.0734-3.19640.29441450.23932727X-RAY DIFFRACTION99
3.1964-3.34180.28271410.21812733X-RAY DIFFRACTION99
3.3418-3.51770.25641420.20482728X-RAY DIFFRACTION99
3.5177-3.73790.19881430.18332719X-RAY DIFFRACTION98
3.7379-4.0260.20061410.17952710X-RAY DIFFRACTION99
4.026-4.43030.20671450.15822727X-RAY DIFFRACTION98
4.4303-5.06940.17731420.15642686X-RAY DIFFRACTION98
5.0694-6.37950.23131430.17712686X-RAY DIFFRACTION97
6.3795-33.1170.17031420.17382665X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.29881.5167-1.07755.5696-0.42083.3467-0.069-0.8592-0.12780.3086-0.0117-1.1660.06290.70120.05030.3921-0.0159-0.02180.614-0.00510.54876.928128.2134-16.2972
23.2645-0.65120.14164.5651-0.18634.1413-0.1039-0.13760.6002-0.2244-0.0308-0.1416-0.89450.28450.09370.5025-0.0569-0.0080.34-0.03280.416566.640937.2008-20.146
32.86661.9961-0.6527.37440.98173.1749-0.33420.2312-0.0304-1.51690.2134-0.33020.06880.36080.12580.7608-0.03210.01950.45350.02720.373167.368723.5529-34.3898
40.52730.085-0.42160.0133-0.06970.37550.06070.5899-0.0283-2.77990.34971.00931.6319-0.8875-0.44181.3811-0.052-0.4030.5884-0.03120.682451.76567.8333-37.5049
53.27781.309-0.00416.394-0.20012.9843-0.06460.0806-0.0633-0.60490.0872-0.2609-0.11420.30150.00430.42370.07650.01760.35220.00280.246665.678519.5031-22.9281
61.4108-0.77330.07530.4807-0.32532.02980.71440.06610.45040.1309-0.292-0.3378-0.99920.3347-0.47371.5604-0.2956-0.00540.51520.00361.364674.736472.3327-25.8907
73.49812.17030.70523.1130.09610.2027-0.14010.6211.2428-1.02210.36430.4669-1.72340.0161-0.3051.8129-0.1536-0.11860.61910.12621.467568.472377.9352-32.6798
82.08311.0167-0.2492.69580.91843.8532-0.18210.46540.55-1.89710.1545-0.009-0.74290.5140.05021.3047-0.11930.10750.57350.05131.068371.441260.6284-34.7839
97.5527-7.8976-2.33172.00183.83973.42250.47110.91030.741-0.547-0.1555-0.0240.3166-0.6486-0.36581.30680.0705-0.3970.9458-0.15571.505752.563158.7419-34.3228
101.73140.177-1.07853.3210.1072.50390.04280.10250.0646-0.83670.14-0.4167-0.0434-0.016-0.07510.9785-0.0803-0.030.43130.09370.826265.347254.4575-29.1456
114.9606-3.4871-4.23143.15732.65173.75240.674-1.69631.13570.79250.2498-1.5703-0.45091.2535-0.88470.8858-0.1537-0.1320.8829-0.13571.138480.117962.3313-21.745
125.08410.68920.04213.5293-0.71245.3119-0.3096-0.41051.2445-0.07110.32570.2096-1.024-0.3440.05240.8160.0855-0.09830.3955-0.07720.973458.542361.7702-19.385
131.64721.2386-0.99231.5764-1.03161.19550.2278-0.01890.29880.1073-0.1156-0.1148-0.9288-0.3306-0.14971.18810.0228-0.17280.7135-0.16931.374256.84271.9019-21.1224
142.48790.083-0.72183.36780.13043.36370.1007-0.1974-0.28650.0327-0.02470.42590.6263-0.4974-0.10960.5258-0.1118-0.07350.50790.13140.44548.2474-14.8618-10.3061
150.89371.45261.11986.16361.0722.60370.1468-0.3761-0.28580.5827-0.0361-0.29690.3235-0.1743-0.13150.4343-0.01410.05510.53480.06920.388254.80361.24882.3449
161.7397-0.0144-0.01434.44651.19342.43980.0116-0.28580.10470.281-0.01320.4720.069-0.3643-0.01810.3757-0.00760.03840.53850.05060.326853.67494.8024-5.9196
172.25351.8175-1.16712.008-0.24362.35610.0848-0.8062-0.92980.27410.29691.65040.9278-1.0867-0.41451.0101-0.4141-0.09371.01270.34931.397327.076-33.2584-4.1652
181.7412.29620.01082.9892-0.31114.18840.5750.4324-1.378-0.20280.24381.85961.2554-0.4584-0.7671.082-0.3475-0.34970.8130.08631.637730.3236-34.0531-12.9569
199.7878-4.90856.2572.5402-2.84625.11030.3462-0.0143-0.4317-0.77190.4441.12590.4007-0.9898-0.7030.7285-0.2912-0.18660.84480.31831.198930.6211-20.0813-18.4444
20-0.0107-0.0010.0179-0.0075-0.0130.02210.46651.0592-1.2338-0.1463-0.00850.58841.2121-0.4771-0.48091.1148-0.3503-0.5391.05060.07321.536623.1456-32.0123-21.7109
210.782-1.7592.11113.9301-4.72635.68360.66120.2002-0.1667-1.4394-1.02021.11750.0251-0.64570.45761.473-0.2994-0.63451.75760.16581.69315.3013-25.459-25.9486
222.5888-1.55680.33611.08560.59052.7336-0.10840.01630.48070.16860.33010.9080.8763-0.3818-0.26271.3986-0.5359-0.27231.1030.16011.698818.5768-40.9228-14.6458
233.99370.7681.04256.1359-2.29931.31760.417-1.03550.22891.50870.46750.677-0.5616-0.9622-0.670.8406-0.02680.2461.4309-0.02180.823638.10722.42069.006
242.07361.3518-0.19614.0058-3.09182.81140.0252-0.01491.1107-0.05660.7671.7526-0.1652-0.8988-0.7020.60950.1342-0.08860.90620.17241.182335.963114.6973-14.4146
255.76084.668-0.24899.2943-3.48654.3247-0.98021.32870.3952-2.02031.38980.6941-0.2811-0.6393-0.36021.341-0.0899-0.21580.77490.03050.64148.603527.9203-40.8078
267.26421.2883-1.76485.61030.29888.7424-0.2230.918-0.5169-1.54170.00110.69150.3295-0.880.30040.8854-0.0109-0.18270.5247-0.01090.603451.624927.3006-39.2539
276.1902-2.3691-2.25479.9359-0.13983.5033-0.0504-0.02220.8524-0.17750.57042.20890.9417-1.167-0.59890.4854-0.0572-0.1420.88410.1331.1437.483515.9886-17.8888
281.8541.5626-0.33645.7055-3.33764.04760.4325-1.3829-0.15881.46980.11531.8234-0.655-0.3009-0.60320.7189-0.06560.25881.4170.18061.154831.42773.02654.6658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 628 through 656 )
2X-RAY DIFFRACTION2chain 'A' and (resid 657 through 762 )
3X-RAY DIFFRACTION3chain 'A' and (resid 763 through 840 )
4X-RAY DIFFRACTION4chain 'A' and (resid 841 through 857 )
5X-RAY DIFFRACTION5chain 'A' and (resid 858 through 912 )
6X-RAY DIFFRACTION6chain 'B' and (resid 178 through 199 )
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 244 )
9X-RAY DIFFRACTION9chain 'B' and (resid 245 through 255 )
10X-RAY DIFFRACTION10chain 'B' and (resid 256 through 270 )
11X-RAY DIFFRACTION11chain 'B' and (resid 271 through 280 )
12X-RAY DIFFRACTION12chain 'B' and (resid 281 through 332 )
13X-RAY DIFFRACTION13chain 'B' and (resid 333 through 379 )
14X-RAY DIFFRACTION14chain 'D' and (resid 628 through 784 )
15X-RAY DIFFRACTION15chain 'D' and (resid 785 through 836 )
16X-RAY DIFFRACTION16chain 'D' and (resid 837 through 912 )
17X-RAY DIFFRACTION17chain 'C' and (resid 187 through 269 )
18X-RAY DIFFRACTION18chain 'C' and (resid 270 through 291 )
19X-RAY DIFFRACTION19chain 'C' and (resid 292 through 301 )
20X-RAY DIFFRACTION20chain 'C' and (resid 302 through 332 )
21X-RAY DIFFRACTION21chain 'C' and (resid 333 through 350 )
22X-RAY DIFFRACTION22chain 'C' and (resid 351 through 378 )
23X-RAY DIFFRACTION23chain 'E' and (resid 422 through 427 )
24X-RAY DIFFRACTION24chain 'E' and (resid 428 through 437 )
25X-RAY DIFFRACTION25chain 'E' and (resid 438 through 446 )
26X-RAY DIFFRACTION26chain 'F' and (resid 422 through 431 )
27X-RAY DIFFRACTION27chain 'F' and (resid 432 through 439 )
28X-RAY DIFFRACTION28chain 'F' and (resid 440 through 446 )

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