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- PDB-6w8j: Structure of DNMT3A (R882H) in complex with CAG DNA -

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Basic information

Entry
Database: PDB / ID: 6w8j
TitleStructure of DNMT3A (R882H) in complex with CAG DNA
Components
  • CAG DNA (25-MER)
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3A
KeywordsTRANSFERASE/DNA / DNA methylation / DNMT3A(R882H) / AML / epigenetics / TRANSFERASE / 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 / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / 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 / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / 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 / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / negative regulation of gene expression, epigenetic / lncRNA binding / 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 / post-embryonic development / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / 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 / nuclear matrix / RMTs methylate histone arginines / 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 / 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: 2.445 Å
AuthorsAnteneh, H. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.
Authors: Anteneh, H. / Fang, J. / Song, J.
History
DepositionMar 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 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 / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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 3A
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
E: CAG DNA (25-MER)
F: CAG DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8888
Polymers129,1196
Non-polymers7692
Water2,720151
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)205.943, 205.943, 89.371
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 32696.668 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 (E. coli)
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 (E. coli) / References: UniProt: Q9UJW3
#3: DNA chain CAG DNA (25-MER)


Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Citrate pH 4.4, 0.2 % PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.5 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5 Å / Relative weight: 1
ReflectionResolution: 2.445→43.35 Å / Num. obs: 52247 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.992 / Net I/σ(I): 7.8
Reflection shellResolution: 2.45→2.54 Å / Num. unique obs: 51900 / CC1/2: 0.404

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XY2

5xy2
PDB Unreleased entry


Resolution: 2.445→43.346 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 1996 3.82 %
Rwork0.1832 50251 -
obs0.1847 52247 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.44 Å2 / Biso mean: 98.6623 Å2 / Biso min: 37.23 Å2
Refinement stepCycle: final / Resolution: 2.445→43.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7255 981 52 151 8439
Biso mean--79.58 83.23 -
Num. residues----989
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4452-2.50640.31861430.28693611
2.5064-2.57410.25811410.25883551
2.5741-2.64990.29061460.24463604
2.6499-2.73540.26971440.24773578
2.7354-2.83310.24991390.24873601
2.8331-2.94660.26641420.24123603
2.9466-3.08060.28731440.22763585
3.0806-3.2430.27091430.23093591
3.243-3.44610.24111410.20343572
3.4461-3.7120.20321420.18223592
3.712-4.08530.20341440.16583608
4.0853-4.67590.20251410.15343595
4.6759-5.88880.22241410.16083570
5.8888-43.3460.19391450.15633590
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)
12.3229-0.1284-0.38764.3198-0.51574.4147-0.0345-0.13820.3638-0.0805-0.0449-0.3871-0.61510.29370.06920.4763-0.0497-0.0150.3675-0.04420.4824172.138-142.72913.921
22.85912.6117-2.17669.3489-0.07423.691-0.50380.4026-0.4914-1.50770.2683-0.76240.6646-0.07990.20350.9454-0.02250.12630.51160.00810.4933170.738-160.2032.138
34.7511.5882-2.29427.1387-1.2783.8785-0.35790.60860.0208-1.13580.33230.0230.4413-0.231-0.02010.6202-0.0080.01320.41650.0160.3107166.087-161.6789.159
43.64490.8796-2.00590.2404-0.541.1271-0.0116-0.46270.51690.26030.21830.0029-1.12021.2779-0.5321.5253-0.32220.15290.7731-0.14331.7911183.658-102.16815.769
54.25881.6599-2.15429.1780.0982.9686-0.01430.32921.0633-1.08340.02630.2091-1.04380.14960.11071.1941-0.0883-0.07560.47010.0150.8671171.923-115.7334.428
68.1003-4.438-3.19688.19291.85995.51280.0533-0.63111.47130.16110.00010.4515-1.2542-0.5010.0350.94580.1142-0.1310.5748-0.18070.9753160.886-115.39817.104
76.44233.4991.92055.33691.3811.7099-0.3418-0.15930.2546-0.9088-0.04940.1674-1.1195-0.33930.35151.31780.11320.01930.7804-0.22511.4442160.68-105.45211.641
81.99362.69213.49123.86295.22787.16110.23970.006-0.9226-0.39940.10182.0980.625-0.8960.04421.1568-0.3842-0.13521.12410.38062.054128.434-220.47226.87
99.15745.58046.88086.32486.23488.4610.02051.4263-0.04791.21180.66751.68820.811-0.809-0.29091.2533-0.6249-0.05971.41650.26332.1359123.017-221.27129.564
105.7822-2.79373.46745.6723-0.05338.2433-0.4203-1.8095-2.37491.77510.43032.49870.04860.3171-0.09251.1534-0.3650.28161.07480.24571.2218135.965-209.17536.675
111.17922.5226-0.80955.861-2.33674.9890.4409-0.942-1.46720.72960.30263.0450.2601-1.7498-0.65991.1504-0.6538-0.38121.02480.39762.1613126.872-208.41127.614
128.6488-0.73070.24890.5639-1.69425.25380.6348-0.2668-1.2654-0.4296-0.24842.65380.8722-0.4345-0.41260.8461-0.3757-0.2290.85220.25931.6929134.214-209.0823.516
137.1084-6.72382.15788.1242-4.74444.8428-0.10260.2482-1.6086-1.02090.60931.53060.3149-0.3873-0.35010.7694-0.3729-0.20310.91780.14811.1569134.151-199.02815.296
146.1242-0.07535.07069.76540.84025.46571.55630.9715-3.45090.82170.02960.7348-0.38530.148-1.67090.9868-0.2832-0.30851.28780.17051.3812125.115-208.68910.78
158.5251-3.20786.53147.4636-7.49749.29551.01790.8706-0.5422-3.0678-0.1052-0.11632.8889-0.3405-1.29261.8811-1.0607-0.93030.71210.37722.4505127.136-212.2669.862
161.7198-0.64613.1043.335-2.00285.8023-0.64141.3766-0.1126-0.5254-0.3252.1318-0.9323-1.39610.91851.1604-0.1752-0.73821.04330.06432.4455115.737-197.84510.026
177.6315-2.9128-0.64591.09490.05187.0046-0.96330.5319-0.5731-2.14131.62070.23022.2018-0.2231-0.95922.0362-1.1095-0.83621.0330.43371.9623123.987-223.00818.646
185.9204-0.36640.33859.0096-1.52095.15720.0511-0.0769-0.2377-0.4175-0.04190.08730.4566-0.0148-0.04140.4125-0.04990.02850.38650.06140.2442158.689-192.21617.871
194.1057-0.7362-1.25184.84770.38485.482-0.0076-0.2718-0.43470.4252-0.01941.02640.3948-0.82730.05550.524-0.16560.05220.66940.17590.6158145.619-194.41429.588
200.45041.16920.51123.08482.52371.99070.0929-0.3533-0.31421.26670.12-0.38420.5602-0.1011-0.25580.7259-0.0484-0.03310.71220.11330.5586158.426-183.12138.3
215.57884.85116.78034.45226.02948.48140.1274-0.86821.06550.2768-0.64381.73050.0769-1.68320.69360.63770.13080.11060.8926-0.00320.8745151.328-166.0734.857
225.36540.26530.69647.36051.68577.1341-0.1638-0.25730.1187-0.330.1190.4674-0.3475-0.47350.09020.35320.02910.02430.46890.04860.3439155.732-169.55625.828
237.6993-6.9001-4.03866.50044.44573.5135-0.3508-1.0566-0.22030.3950.9126-0.63590.31420.5341-0.55580.6737-0.0739-0.06940.7210.0810.5179165.666-192.6431.747
247.1792-1.08624.20919.6054-5.528.89060.3604-0.28981.20110.28780.26041.1008-2.0512-0.3227-0.64660.9960.11430.30531.21820.08641.2598137.209-171.06130.754
256.89355.8516-5.18017.6922-6.46615.9936-0.51270.5686-0.097-0.6990.8960.16810.4591-0.219-0.36950.980.115-0.19391.2445-0.10660.7907150.625-152.447-1.561
267.92833.7105-3.12547.7801-8.18818.1498-0.08550.22960.2456-0.65710.93661.30330.6349-1.2902-0.73840.7468-0.0648-0.17250.95-0.10910.7667148.224-156.0523.611
274.1129-4.64881.43199.10294.53992.00970.5698-0.9717-0.6303-0.48270.42741.3361-3.933-0.5092-0.9051.86920.22010.28161.90240.10391.3229133.186-168.11932.522
285.7176-0.5038-4.46474.26235.9441.9978-0.0971-0.6834-0.00161.66930.2027-0.68470.932-0.0684-0.15841.3059-0.13860.20411.50480.27231.6174135.181-182.40543.201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 629:784 )A629 - 784
2X-RAY DIFFRACTION2( CHAIN A AND RESID 785:839 )A785 - 839
3X-RAY DIFFRACTION3( CHAIN A AND RESID 840:912 )A840 - 912
4X-RAY DIFFRACTION4( CHAIN B AND RESID 178:191 )B178 - 191
5X-RAY DIFFRACTION5( CHAIN B AND RESID 192:280 )B192 - 280
6X-RAY DIFFRACTION6( CHAIN B AND RESID 281:339 )B281 - 339
7X-RAY DIFFRACTION7( CHAIN B AND RESID 340:380 )B340 - 380
8X-RAY DIFFRACTION8( CHAIN C AND RESID 185:199 )C185 - 199
9X-RAY DIFFRACTION9( CHAIN C AND RESID 200:221 )C200 - 221
10X-RAY DIFFRACTION10( CHAIN C AND RESID 222:234 )C222 - 234
11X-RAY DIFFRACTION11( CHAIN C AND RESID 235:255 )C235 - 255
12X-RAY DIFFRACTION12( CHAIN C AND RESID 256:291 )C256 - 291
13X-RAY DIFFRACTION13( CHAIN C AND RESID 292:301 )C292 - 301
14X-RAY DIFFRACTION14( CHAIN C AND RESID 302:319 )C302 - 319
15X-RAY DIFFRACTION15( CHAIN C AND RESID 320:339 )C320 - 339
16X-RAY DIFFRACTION16( CHAIN C AND RESID 340:353 )C340 - 353
17X-RAY DIFFRACTION17( CHAIN C AND RESID 354:378 )C354 - 378
18X-RAY DIFFRACTION18( CHAIN D AND RESID 628:698 )D628 - 698
19X-RAY DIFFRACTION19( CHAIN D AND RESID 699:784 )D699 - 784
20X-RAY DIFFRACTION20( CHAIN D AND RESID 785:818 )D785 - 818
21X-RAY DIFFRACTION21( CHAIN D AND RESID 819:849 )D819 - 849
22X-RAY DIFFRACTION22( CHAIN D AND RESID 850:894 )D850 - 894
23X-RAY DIFFRACTION23( CHAIN D AND RESID 895:912 )D895 - 912
24X-RAY DIFFRACTION24( CHAIN E AND RESID 423:433 )E423 - 433
25X-RAY DIFFRACTION25( CHAIN E AND RESID 434:447 )E434 - 447
26X-RAY DIFFRACTION26( CHAIN F AND RESID 423:438 )F423 - 438
27X-RAY DIFFRACTION27( CHAIN F AND RESID 439:443 )F439 - 443
28X-RAY DIFFRACTION28( CHAIN F AND RESID 444:446 )F444 - 446

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