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- PDB-8ba5: Crystal structure of the DNMT3A ADD domain -

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Basic information

Entry
Database: PDB / ID: 8ba5
TitleCrystal structure of the DNMT3A ADD domain
ComponentsDNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5)-methyltransferase 3A
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


: / positive regulation of cellular response to hypoxia / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity ...: / positive regulation of cellular response to hypoxia / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / XY body / DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / cellular response to ethanol / response to vitamin A / : / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / response to cocaine / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to amino acid stimulus / response to lead ion / euchromatin / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / transcription corepressor activity / response to estradiol / cellular response to hypoxia / spermatogenesis / 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 / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLinhard, V. / Kunert, S. / Wollenhaupt, J. / Broehm, A. / Schwalbe, H. / Jeltsch, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)JE 252/10 Germany
CitationJournal: Protein Sci. / Year: 2023
Title: The MECP2-TRD domain interacts with the DNMT3A-ADD domain at the H3-tail binding site.
Authors: Kunert, S. / Linhard, V. / Weirich, S. / Choudalakis, M. / Osswald, F. / Kramer, L. / Kohler, A.R. / Brohm, A. / Wollenhaupt, J. / Schwalbe, H. / Jeltsch, A.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6567
Polymers16,3121
Non-polymers3456
Water2,126118
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)57.800, 57.800, 138.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-706-

MG

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3A / DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / Cysteine methyltransferase DNMT3A / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA


Mass: 16311.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 17 % PEG 8000, 0.2 M Magnesiumsulfat, 0.1 M TRIS-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.45→47.08 Å / Num. obs: 45978 / % possible obs: 99.8 % / Redundancy: 20.7 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 1 / Net I/σ(I): 17.62
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 20.86 % / Mean I/σ(I) obs: 1.24 / Num. unique obs: 7353 / CC1/2: 0.67 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A1A

3a1a


Resolution: 1.45→22 Å / SU ML: 0.1969 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2129 1590 3.46 %
Rwork0.1867 44319 -
obs0.1876 45909 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.89 Å2
Refinement stepCycle: LAST / Resolution: 1.45→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 12 118 1180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531115
X-RAY DIFFRACTIONf_angle_d0.80551503
X-RAY DIFFRACTIONf_chiral_restr0.0786153
X-RAY DIFFRACTIONf_plane_restr0.0075201
X-RAY DIFFRACTIONf_dihedral_angle_d12.1614418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50.34821440.31284009X-RAY DIFFRACTION100
1.5-1.550.30171440.26894032X-RAY DIFFRACTION99.95
1.55-1.610.26861460.24124071X-RAY DIFFRACTION100
1.61-1.690.25491380.20963992X-RAY DIFFRACTION100
1.69-1.770.25131440.20374037X-RAY DIFFRACTION100
1.77-1.890.24821390.19764021X-RAY DIFFRACTION99.98
1.89-2.030.19271450.18174040X-RAY DIFFRACTION100
2.03-2.240.18631480.18684028X-RAY DIFFRACTION100
2.24-2.560.20581480.18834018X-RAY DIFFRACTION100
2.56-3.220.25061500.18024047X-RAY DIFFRACTION100
3.22-220.17731440.16644024X-RAY DIFFRACTION100
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)
13.642493433311.88635170015-0.4979097162386.37407562451-2.370143725080.896611749807-0.4904595839220.9780832572850.435923779727-0.4659025341480.00637205798965-0.561426572494-0.4502423400040.9649330588780.3602554031090.304025230861-0.113251707611-0.04096131492240.3129137334830.06434416580360.2661877637277.00105410725-12.032066706-6.62249770814
24.300079332782.22915039965-0.8883528566696.93518789364-0.9154555256293.21799248602-0.505812324808-0.1810261895650.5862701244920.150477090035-0.127910854758-0.644381345064-0.6567067604460.306379730451-0.1186927899180.433282881113-0.0921589256105-0.2087115097260.2270333973940.01696854670190.3351278715218.41388351044-6.916246934040.853330429158
32.45720155722-0.4236881509690.7727035297121.1486493622-0.1085932506062.25180363093-0.390514459363-0.1818133020970.4047651792450.0245326366819-0.09587455140870.0103123807257-0.911697310227-0.1957731314880.2505460855060.3269468882620.0244328515792-0.08066129200070.199314878056-0.05034670684090.23653078268-3.60981781429-9.16262702229-0.642068438497
43.345177240413.818734324172.040175366755.105528842251.24452996153.36533899357-0.303062476151-0.24591121090.2296973649120.00347946487202-0.009617299917140.213621729855-0.279065646218-0.5345820981530.3188688040840.3604397383540.0899723466688-0.0416743308720.253956278116-0.01422664357590.256824092339-12.229636322-10.4814594088-4.26425528172
55.309758652070.636122797015-1.378758438928.112000778322.554464746465.258301572420.04194808510750.018014135777-0.0580834274596-0.124071410884-0.09762088421590.0562095117336-0.0745663696125-0.09347161195890.05851676576810.14559735756-0.003580109808350.01594727113710.233774345663-0.01573352094630.199045781215-16.664638845-27.0575348686-3.11973395565
64.268290507970.6477369925780.4919645616972.517167657790.301605323122.430627978020.103344885179-0.3614134400270.02797690474210.148522070076-0.1151479383770.08099735078720.0446174578728-0.09203733079790.001103202760920.1147340327750.00736954648209-0.01634486307310.170901925812-0.01085821143340.147003063939-6.60891761102-25.0868067872-2.8816681133
73.368644607083.75252321133-1.945786447084.64738239589-2.26067182547.03282583093-0.2647607064560.291135361074-0.914518393628-0.663976303860.0195064034176-0.1880243846340.2952652650990.1914073163080.1367317546530.119461394740.0546905680143-0.01625915696320.227990428775-0.04355536999360.2946012631335.75749112451-27.9716879328-2.60349921085
88.562717162471.24500618682-1.923968121618.735453504332.028810530712.12321016684-0.117152086413-0.319471388019-1.096265215980.31847295801-0.12755318627-0.4361946616730.583416440657-0.2650627022190.2132156346310.324452251053-0.0612449259442-0.01364997353610.3300686048440.02666353189580.328706903967-3.47126736379-29.98815357085.06702333204
93.729536642241.0199699535-3.18890880074.903573729611.028260324845.562343257890.0132787510811-0.8389654166730.1035284152270.502629366216-0.216889261967-0.04147975958810.0700645089246-0.4332034158930.1814997352930.177982289264-0.00487891171034-0.06030492590540.392102261841-0.0459091541350.1652330107630.161357159653-19.07397474199.77434297529
109.28790851175-5.583483997855.295982698853.40239926732-3.319993680633.40612837427-0.401077131909-0.6327265084920.626500152115-0.1349583248860.4897973755860.197936286605-0.815779600412-0.285353762942-0.1011524839910.4469580119670.1074703867020.002695304426340.515211896729-0.04113020157980.315471816306-13.3484527416-12.83658292858.65932587465
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 474 through 484 )474 - 4841 - 11
22chain 'A' and (resid 485 through 492 )485 - 49212 - 19
33chain 'A' and (resid 493 through 511 )493 - 51120 - 38
44chain 'A' and (resid 512 through 524 )512 - 52439 - 51
55chain 'A' and (resid 525 through 534 )525 - 53452 - 61
66chain 'A' and (resid 535 through 566 )535 - 56662 - 93
77chain 'A' and (resid 567 through 575 )567 - 57594 - 102
88chain 'A' and (resid 576 through 587 )576 - 587103 - 112
99chain 'A' and (resid 588 through 600 )588 - 600113 - 125
1010chain 'A' and (resid 601 through 609 )601 - 609126 - 134

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