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- PDB-6kda: Crystal structure of human DNMT3B-DNMT3L in complex with DNA cont... -

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Basic information

Entry
Database: PDB / ID: 6kda
TitleCrystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site
Components
  • DNA (25-MER)
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE/DNA / DNMT3B / DNA methyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / DNA methylation / placenta development / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / stem cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / enzyme activator activity / NoRC negatively regulates rRNA expression / transcription corepressor activity / spermatogenesis / methylation / negative regulation of DNA-templated transcription / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / 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. ...DNA (cytosine-5)-methyltransferase 3B, ADD domain / 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 3B / DNA (cytosine-5)-methyltransferase 3-like
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 Å
AuthorsLin, C.-C. / Chen, Y.-P. / Yang, W.-Z. / Shen, C.-K. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
Authors: Lin, C.C. / Chen, Y.P. / Yang, W.Z. / Shen, J.C.K. / Yuan, H.S.
History
DepositionJul 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 3B
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3B
E: DNA (25-MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8478
Polymers128,0786
Non-polymers7692
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-59 kcal/mol
Surface area48170 Å2
Unit cell
Length a, b, c (Å)193.872, 193.872, 49.741
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3B / Dnmt3b / DNA methyltransferase HsaIIIB / M.HsaIIIB


Mass: 32715.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 23627.107 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 DNA (25-MER)


Mass: 7696.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.29 Å3/Da / Density % sol: 71.36 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0 mM MES (pH 5.7), 160 mM KCl, 10 mM MgSO4 and 14% PEG 400

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.909→30 Å / Num. obs: 42182 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.972 / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.95
Reflection shellResolution: 2.91→3.01 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 2208 / CC1/2: 0.852 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YX2

5yx2


Resolution: 2.909→29.5 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.99
RfactorNum. reflection% reflection
Rfree0.2199 2100 4.98 %
Rwork0.1876 --
obs0.1892 42169 91.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 245.46 Å2 / Biso min: 8.51 Å2
Refinement stepCycle: final / Resolution: 2.909→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7625 1022 52 305 9004
Biso mean--26.6 43.38 -
Num. residues----989
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9094-2.9770.320885130346
2.977-3.05140.260280168058
3.0514-3.13380.2257118226878
3.1338-3.22590.2566177287799
3.2259-3.32990.25081532877100
3.3299-3.44870.29131142937100
3.4487-3.58660.27822002891100
3.5866-3.74950.22721912847100
3.7495-3.94670.24821572900100
3.9467-4.19340.21081150.16622949100
4.1934-4.51610.19411780.14992899100
4.5161-4.96860.19831520.15512899100
4.9686-5.68310.18651042943100
5.6831-7.14330.20241442928100
7.14330.16891320.185287199
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)
15.76240.76480.33273.0167-0.38664.06250.0760.1264-0.3174-0.0609-0.11710.55760.3107-0.42160.05620.3619-0.1877-0.08520.2962-0.05620.345313.7513-79.0635-10.4383
23.86091.35411.47132.39410.43882.89760.3078-0.6466-0.39610.6797-0.21860.3475-0.03660.0845-0.11130.4828-0.19010.01790.51480.05260.094527.0664-72.41353.6671
33.89181.48484.50758.03584.75056.45750.1247-0.04930.2429-0.01670.08690.95460.2626-0.9728-0.14390.5025-0.2811-0.18291.1437-0.25551.7407-22.4276-88.0278-20.3169
49.43851.49272.47774.4461-0.81356.3082-0.1648-0.15650.84830.0891-0.21341.0164-0.1659-0.73940.33470.3395-0.1028-0.07210.7157-0.26491.1011-9.9808-78.9592-13.1398
54.4084-5.14414.23546.0894-4.71914.4951-0.5085-0.06561.39380.04470.45440.7989-0.7791-0.92440.09330.74590.0075-0.48831.15520.05181.8924-14.3754-68.087-26.5519
69.3108-4.5605-0.25093.6946-0.08784.9498-0.03991.28852.0097-0.9442-0.28850.7303-0.6971-0.85270.37210.6825-0.0575-0.58441.09370.16151.6306-13.6577-70.9194-26.3994
74.85691.403-1.66324.42160.32083.9277-0.08190.29090.6244-0.0891-0.29961.5564-0.7008-0.66360.36851.02360.073-0.46131.1773-0.03212.6048-16.3863-58.2897-19.6318
86.20843.96491.93635.11081.02092.9997-0.12190.32171.1172-0.29570.09541.3711-0.0396-0.9380.13550.7611-0.1993-0.47911.2795-0.12541.8061-24.2806-82.6689-25.9339
94.08481.02911.56750.89751.33532.86930.1596-0.51870.6380.09870.18090.0238-0.57690.4216-0.25740.7129-0.4686-0.43640.95390.02531.681186.657-25.26319.6124
107.1342.01720.10744.6743-1.0580.29030.14890.2131.3399-0.52650.1374-0.8101-1.20011.375-0.30831.2366-0.614-0.35461.30210.0992.071691.7478-19.63732.5317
115.65664.00290.30256.39283.05025.6738-0.51630.78720.6187-0.83490.4752-0.4924-0.75590.8885-0.0810.538-0.3163-0.24310.73370.09591.293981.0007-31.2816-3.589
121.0637-0.7401-0.18094.18821.13620.307-0.18950.95922.6718-1.7454-0.34141.5577-2.3049-1.07750.53851.28220.0349-0.60390.93070.29582.235564.177-20.3833-4.1353
135.23714.99180.07696.19013.1766.7786-0.1837-0.08860.84120.2064-0.14160.1144-0.1930.22040.25940.507-0.2038-0.23610.4970.00791.089473.8913-32.67133.9284
140.13820.06-0.81492.00474.62937.15710.0226-0.45111.97790.4764-0.40271.2212-0.7345-0.85430.40530.7153-0.1297-0.21970.7836-0.31451.611963.5847-27.927710.9335
151.0425-0.9296-0.48332.00391.80061.14280.0102-0.92641.09991.1318-0.43251.8041-0.6087-0.48040.47021.1101-0.247-0.15080.9089-0.52981.74668.5307-23.301315.1649
164.52546.0519-5.21428.9903-5.20769.4002-0.096-0.18730.436-0.07090.25410.3679-0.309-0.863-0.09981.1378-0.0986-0.04661.0235-0.70872.792655.9947-15.43239.6295
177.085-0.5120.53132.72040.99283.64390.4762-0.31370.52270.2517-0.41790.9881-0.78090.26690.06151.0127-0.3499-0.3481.0176-0.35431.749283.743-20.29213.9684
184.35361.60390.00454.30820.3644.3615-0.0494-0.00670.31220.2463-0.0155-0.5989-0.21090.39350.06420.1473-0.0696-0.07110.4873-0.05390.350461.5693-51.4408-1.6961
193.36471.37930.8082.72411.07362.7469-0.14540.9440.1667-0.38410.1771-0.6405-0.033-0.0469-0.06860.3317-0.12310.05030.6621-0.01330.045449.1917-59.6406-15.8285
205.4605-1.56442.77318.0254.18864.6769-0.04020.68631.4821-0.8620.29991.96580.3825-1.3723-0.28161.2167-0.01050.21321.50060.72181.792439.4004-41.9006-17.2782
218.95016.8862-5.15145.8503-5.266.0781.2837-0.55283.58271.4606-0.61742.1636-2.46312.2734-0.64341.7878-0.59230.16441.56590.05952.153711.7898-57.44688.194
229.3729-1.49972.725.3899-1.06245.2220.5153-1.31962.93121.0787-0.67110.349-1.29841.23220.09621.492-0.20080.49611.2316-0.18391.638116.5459-55.07415.1491
239.9389-3.6202-5.15342.019-1.9672.01880.14142.22133.8546-0.17470.62311.99110.5478-2.8768-0.78521.1889-0.11210.05841.95840.08192.15443.8414-38.9136-20.4091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 570 through 725 )A570 - 725
2X-RAY DIFFRACTION2chain 'A' and (resid 726 through 853 )A726 - 853
3X-RAY DIFFRACTION3chain 'B' and (resid 176 through 217 )B176 - 217
4X-RAY DIFFRACTION4chain 'B' and (resid 218 through 301 )B218 - 301
5X-RAY DIFFRACTION5chain 'B' and (resid 302 through 318 )B302 - 318
6X-RAY DIFFRACTION6chain 'B' and (resid 319 through 339 )B319 - 339
7X-RAY DIFFRACTION7chain 'B' and (resid 340 through 360 )B340 - 360
8X-RAY DIFFRACTION8chain 'B' and (resid 361 through 379 )B361 - 379
9X-RAY DIFFRACTION9chain 'C' and (resid 178 through 206 )C178 - 206
10X-RAY DIFFRACTION10chain 'C' and (resid 207 through 217 )C207 - 217
11X-RAY DIFFRACTION11chain 'C' and (resid 218 through 244 )C218 - 244
12X-RAY DIFFRACTION12chain 'C' and (resid 245 through 255 )C245 - 255
13X-RAY DIFFRACTION13chain 'C' and (resid 256 through 291 )C256 - 291
14X-RAY DIFFRACTION14chain 'C' and (resid 292 through 318 )C292 - 318
15X-RAY DIFFRACTION15chain 'C' and (resid 319 through 339 )C319 - 339
16X-RAY DIFFRACTION16chain 'C' and (resid 340 through 360 )C340 - 360
17X-RAY DIFFRACTION17chain 'C' and (resid 361 through 379 )C361 - 379
18X-RAY DIFFRACTION18chain 'D' and (resid 570 through 725 )D570 - 725
19X-RAY DIFFRACTION19chain 'D' and (resid 726 through 853 )D726 - 853
20X-RAY DIFFRACTION20chain 'E' and (resid 422 through 436 )E422 - 436
21X-RAY DIFFRACTION21chain 'E' and (resid 437 through 446 )E437 - 446
22X-RAY DIFFRACTION22chain 'F' and (resid 422 through 436 )F422 - 436
23X-RAY DIFFRACTION23chain 'F' and (resid 437 through 446 )F437 - 446

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