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- PDB-6brr: Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA co... -

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Basic information

Entry
Database: PDB / ID: 6brr
TitleCrystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites
Components
  • DNA (25-MER)
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3A
KeywordsTRANSFERASE/DNA / DNMT3A / DNMT3L / DNA methylation / TRANSFERASE-DNA complex
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / genomic imprinting / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity ...negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / genomic imprinting / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / ESC/E(Z) complex / SUMOylation of DNA methylation proteins / XY body / response to vitamin A / hepatocyte apoptotic process / negative regulation of gene expression via chromosomal CpG island methylation / DNA methylation-dependent constitutive heterochromatin formation / response to ionizing radiation / lncRNA binding / negative regulation of gene expression, epigenetic / male meiosis I / cellular response to ethanol / chromosome, centromeric region / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / stem cell differentiation / DNA methylation / condensed nuclear chromosome / PRC2 methylates histones and DNA / Defective pyroptosis / response to cocaine / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / response to lead ion / response to toxic substance / enzyme activator activity / neuron differentiation / nuclear matrix / RMTs methylate histone arginines / transcription corepressor activity / response to estradiol / methylation / 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 / 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 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 (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: 2.97 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
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / 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 1.2Oct 4, 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
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)129,7538
Polymers128,9856
Non-polymers7692
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-62 kcal/mol
Surface area44890 Å2
Unit cell
Length a, b, c (Å)205.005, 205.005, 89.358
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 32629.602 Da / Num. of mol.: 2 / Mutation: R836A
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: 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) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJW3
#3: DNA chain DNA (25-MER)


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


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has protein modificationN
Sequence detailsthere is apparently an error in the reference sequence Q9Y6K1, as Ser 332 was not observed in any ...there is apparently an error in the reference sequence Q9Y6K1, as Ser 332 was not observed in any other published DNMT3L structures

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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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 7.0), 200 mM NaH2PO4 and 5% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.97→20 Å / Num. obs: 28270 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.3
Reflection shellResolution: 2.97→3.06 Å / Rmerge(I) obs: 1.205

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Processing

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

2qrv


Resolution: 2.97→19.955 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1994 7.05 %
Rwork0.1987 --
obs0.2017 28270 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.97→19.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7182 1020 52 0 8254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048574
X-RAY DIFFRACTIONf_angle_d0.66511868
X-RAY DIFFRACTIONf_dihedral_angle_d19.8693154
X-RAY DIFFRACTIONf_chiral_restr0.0281305
X-RAY DIFFRACTIONf_plane_restr0.0031352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9701-3.04420.34361350.3311848X-RAY DIFFRACTION97
3.0442-3.12620.37321480.31541910X-RAY DIFFRACTION99
3.1262-3.21780.34011410.30571903X-RAY DIFFRACTION99
3.2178-3.32120.30821430.27531893X-RAY DIFFRACTION99
3.3212-3.43930.2971430.24091860X-RAY DIFFRACTION97
3.4393-3.57630.27141460.23321904X-RAY DIFFRACTION99
3.5763-3.73810.27321440.2151876X-RAY DIFFRACTION99
3.7381-3.93370.23281450.20131910X-RAY DIFFRACTION99
3.9337-4.17810.24741450.18881870X-RAY DIFFRACTION99
4.1781-4.49720.20071460.17271880X-RAY DIFFRACTION98
4.4972-4.94360.22521430.17311875X-RAY DIFFRACTION98
4.9436-5.64470.25391400.18821840X-RAY DIFFRACTION97
5.6447-7.0590.23951380.2031878X-RAY DIFFRACTION98
7.059-19.9550.1961370.16311829X-RAY DIFFRACTION95
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)
11.7149-2.3197-0.28864.8522.33061.9607-0.01740.1802-1.01170.24220.05460.57470.8185-0.5450.26070.9777-0.02380.03480.7918-0.03160.9811-13.8993-80.376119.8529
24.935-0.4317-0.45193.30550.43094.27920.16790.4914-0.5705-0.1331-0.2232-0.40540.5590.55560.06520.67380.112-0.03360.73870.00530.7385-1.2697-76.57513.2259
35.9786-2.59930.19144.29911.77223.8750.5311.3599-0.1258-0.8776-0.63550.3827-0.0517-0.35030.05550.72120.1401-0.01651.0431-0.04770.7248-17.8383-63.95241.8312
44.7167-0.808-0.81334.60420.14333.09490.30460.32210.0389-0.0617-0.22150.12520.1597-0.1430.00330.6172-0.0293-0.01130.8764-0.01130.5488-16.5476-65.032412.4621
54.5256-2.26151.55164.4415-0.152.82250.23140.5673-1.83461.7551-0.1635-0.25742.38531.5055-0.07651.92280.6779-0.32851.4077-0.06031.714126.094-107.521614.4607
60.57571.3370.2523.44651.21373.77430.88651.10530.3254-0.3187-0.9991-1.76621.41552.74450.02380.95840.55710.00891.75170.19791.60828.4624-90.8243.9043
74.0897-1.68810.12684.94430.42923.49330.25510.298-0.3682-0.4106-0.4855-0.37740.31750.45570.37970.73810.22410.03481.11960.04491.185819.5763-86.62788.5643
89.25954.44428.312.40693.95437.55130.20161.199-1.31931.1782-0.00520.2728-0.46871.9979-0.16840.76680.2505-0.09121.83960.10771.615532.4517-79.598516.5076
91.89210.6460.4352.26550.5730.2326-0.29650.1065-0.00280.0768-0.0193-0.89480.10440.49560.44931.3801-0.0868-0.06721.29130.3651.644131.7555-78.771120.2921
102.6494-3.64010.53824.2295-0.27590.4017-0.23080.4037-0.2273-0.03380.0591-0.80710.23040.91180.25661.32620.29660.03611.39910.27161.519233.9301-92.245312.0676
114.7041-1.11650.17162.24710.49262.99960.20970.19620.2119-0.10310.00910.0056-0.3866-0.3301-0.06750.7780.02860.0830.6978-0.03250.6631-38.9739-40.783618.9241
123.5524-0.26450.87941.99380.33412.183-0.0656-0.12631.12160.1485-0.1013-0.1068-0.6912-0.03790.05581.0990.03910.12210.6765-0.04440.9774-35.6231-29.082628.6289
134.2372-2.20542.55251.3101-1.4271.2031-0.9817-0.69180.3491.71331.09090.1596-1.1111-0.35640.01511.33960.04060.12740.8942-0.18240.9375-33.5975-29.510839.3048
145.7703-3.03270.55952.1236-1.54232.4467-0.1829-0.2446-0.23640.38770.25440.5738-0.3626-0.2214-0.08890.9982-0.10240.03560.8464-0.10260.8399-31.8799-46.256139.4425
153.3437-0.3304-0.194.0566-1.11232.8997-0.1935-0.37680.22180.67650.1409-1.1763-0.21450.4052-0.05660.8965-0.1051-0.05680.9076-0.13530.9617-11.6919-51.152836.7867
163.2451-2.12671.21323.03670.73091.9393-0.0093-0.39310.16780.20250.112-0.1238-0.5047-0.1254-0.02880.7244-0.03710.03510.6278-0.09170.5918-28.1416-48.22827.7322
170.6778-0.750.91561.0454-1.13521.33980.4569-0.61.8072-0.3325-0.0635-0.3328-1.0728-0.31660.02331.77980.31050.00161.0115-0.1832.184-48.4331-1.100830.4658
181.92510.07450.47833.44780.41473.94380.2480.05161.37690.16240.23970.1257-0.8202-0.213-0.24831.29540.16740.23790.669-0.00291.6183-41.2251-9.371927.0729
191.93512.04761.99082.0145-7.38034.7392-0.7131-0.12781.14760.10980.50872.56110.07432.2213-1.52321.72040.15260.59460.89630.32722.1158-34.8205-0.659714.9841
204.7387-3.10335.6278.8209-2.35627.24220.38952.35751.05-0.72321.40010.2907-2.3651-1.7831-0.23241.84470.25150.44782.01050.09721.4383-43.3438-2.243510.2538
214.89316.4047-2.04828.4845-2.60090.86641.01721.33420.4724-0.059-0.0753-1.2682-1.47070.0267-0.36372.0275-0.11220.5141.1140.43811.7129-24.1171-1.607110.9318
221.312-1.83460.96872.307-1.04741.59570.4747-0.8691-1.371-0.6819-0.1676-0.5462-0.6187-0.2232-0.2851.91860.22070.40630.9448-0.01481.7047-43.07554.034820.7668
230.94640.0015-0.07130.35660.42640.26362.2031-2.41940.50921.18191.4519-1.3265-0.12430.3542-0.33751.7237-0.1098-0.2321.4885-0.32471.4319-15.8014-33.702947.5066
241.4294-0.8117-0.40660.79020.4302-0.16690.6062-0.1140.949-0.1671-0.0416-1.1553-0.5230.4106-0.36631.0499-0.22390.13241.18090.03311.5533-4.9897-36.332623.9749
251.1773-0.5314-2.96041.59282.50537.78491.16570.74310.7864-0.26150.0091-0.6175-0.92930.4538-0.77131.0576-0.05730.18471.45770.15741.1661-5.3271-46.94355.8017
263.6272-4.4931-1.16226.55760.60165.56650.66310.48180.6052-2.1039-0.34290.4051-0.22060.0342-0.62461.36470.25840.14711.74750.0511.30032.0133-60.8387-7.8463
274.2527-1.6416-3.4314.3092-1.45285.40860.26170.82750.7751-0.3293-0.5027-0.4624-0.18620.49110.14620.77860.07520.20881.15320.20611.0323-1.8795-55.1659-1.2477
282.7217-1.2106-1.8033.16933.0251.29930.2556-0.4021.29260.63660.4296-1.0719-0.01330.1561-0.77421.4465-0.2279-0.07511.0406-0.15831.4531-10.1057-34.242631.8373
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 784 )
3X-RAY DIFFRACTION3chain 'A' and (resid 785 through 852 )
4X-RAY DIFFRACTION4chain 'A' and (resid 853 through 912 )
5X-RAY DIFFRACTION5chain 'B' and (resid 179 through 191 )
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 205 )
7X-RAY DIFFRACTION7chain 'B' and (resid 206 through 311 )
8X-RAY DIFFRACTION8chain 'B' and (resid 312 through 325 )
9X-RAY DIFFRACTION9chain 'B' and (resid 326 through 349 )
10X-RAY DIFFRACTION10chain 'B' and (resid 350 through 379 )
11X-RAY DIFFRACTION11chain 'D' and (resid 628 through 698 )
12X-RAY DIFFRACTION12chain 'D' and (resid 699 through 762 )
13X-RAY DIFFRACTION13chain 'D' and (resid 763 through 784 )
14X-RAY DIFFRACTION14chain 'D' and (resid 785 through 818 )
15X-RAY DIFFRACTION15chain 'D' and (resid 819 through 857 )
16X-RAY DIFFRACTION16chain 'D' and (resid 858 through 912 )
17X-RAY DIFFRACTION17chain 'C' and (resid 186 through 201 )
18X-RAY DIFFRACTION18chain 'C' and (resid 202 through 309 )
19X-RAY DIFFRACTION19chain 'C' and (resid 310 through 325 )
20X-RAY DIFFRACTION20chain 'C' and (resid 326 through 339 )
21X-RAY DIFFRACTION21chain 'C' and (resid 340 through 348 )
22X-RAY DIFFRACTION22chain 'C' and (resid 349 through 378 )
23X-RAY DIFFRACTION23chain 'E' and (resid 422 through 426 )
24X-RAY DIFFRACTION24chain 'E' and (resid 428 through 435 )
25X-RAY DIFFRACTION25chain 'E' and (resid 436 through 440 )
26X-RAY DIFFRACTION26chain 'E' and (resid 441 through 446 )
27X-RAY DIFFRACTION27chain 'F' and (resid 422 through 433 )
28X-RAY DIFFRACTION28chain 'F' and (resid 434 through 446 )

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