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- PDB-8zlk: PWWP domain from human DNMT3B -

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Basic information

Entry
Database: PDB / ID: 8zlk
TitlePWWP domain from human DNMT3B
ComponentsDNA (cytosine-5)-methyltransferase 3B
KeywordsDNA BINDING PROTEIN / Methyltransferase / DNA methylation
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA ...DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression / transcription corepressor activity / methylation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
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 / Zinc finger, FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsCho, C.-C. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Sci Adv / Year: 2025
Title: Histone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.
Authors: Cho, C.C. / Huang, H.H. / Jiang, B.C. / Yang, W.Z. / Chen, Y.N. / Yuan, H.S.
History
DepositionMay 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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 3B


Theoretical massNumber of molelcules
Total (without water)33,5122
Polymers33,5122
Non-polymers00
Water25214
1
A: DNA (cytosine-5)-methyltransferase 3B


Theoretical massNumber of molelcules
Total (without water)16,7561
Polymers16,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 3B


Theoretical massNumber of molelcules
Total (without water)16,7561
Polymers16,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.940, 73.940, 156.973
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 16755.896 Da / Num. of mol.: 2 / Fragment: PWWP domain
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: Lithium sulfate monohydrate, CAPS, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→30 Å / Num. obs: 13596 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.74-2.8410.10.49613460.9550.9880.1620.5231.145100
2.84-2.9510.10.36413170.980.9950.1190.3841.224100
2.95-3.09100.27513270.9830.9960.090.291.274100
3.09-3.259.90.17113270.9930.9980.0560.181.262100
3.25-3.459.80.1113430.9970.9990.0360.1161.257100
3.45-3.729.80.07213500.99810.0240.0761.281100
3.72-4.099.70.05413510.99910.0180.0571.18399.9
4.09-4.689.60.04813750.99910.0160.051.28899.9
4.68-5.8910.30.03713760.99910.0120.0391.102100
5.89-3010.60.031484110.0090.0311.25299.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→28.19 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 1311 10.04 %
Rwork0.2208 --
obs0.2256 13059 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 0 14 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032220
X-RAY DIFFRACTIONf_angle_d0.722984
X-RAY DIFFRACTIONf_dihedral_angle_d18.611794
X-RAY DIFFRACTIONf_chiral_restr0.045294
X-RAY DIFFRACTIONf_plane_restr0.004372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.850.361320.3021187X-RAY DIFFRACTION89
2.85-2.980.30711420.27251226X-RAY DIFFRACTION93
2.98-3.140.33341440.26241250X-RAY DIFFRACTION95
3.14-3.340.2851430.25341281X-RAY DIFFRACTION96
3.34-3.590.25591440.22891289X-RAY DIFFRACTION97
3.6-3.960.27241400.20821327X-RAY DIFFRACTION98
3.96-4.530.21311540.19421350X-RAY DIFFRACTION99
4.53-5.690.23171510.19861384X-RAY DIFFRACTION99
5.71-28.190.30081610.22061454X-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)
13.8510.6444-6.10368.1908-1.35169.73930.1333-0.89962.07130.17930.6075-0.505-0.78310.9032-0.6840.79670.0189-0.24160.5895-0.07710.8488-33.530424.44972.5948
25.9521.80191.74035.8033-5.27246.881-0.1922.1561-1.0796-0.65320.81590.39591.43761.1424-0.67080.6436-0.05310.0090.6854-0.06540.4078-47.314118.6411-6.7114
39.89670.1924-3.89019.53030.39315.2071-0.5806-0.2569-0.37060.65440.0287-0.8060.5880.69950.52730.44830.0193-0.0350.3630.05450.2939-34.57315.4048-2.452
48.4444-3.0392-1.9662.05252.47335.4681-0.00740.62240.9160.0239-0.2019-0.19360.0776-0.32750.23370.5155-0.0355-0.0720.38240.12860.4014-46.13319.1023-2.6102
59.7745-4.2899-1.63527.0831-0.57563.6322-0.4063-0.2592-1.8170.320.08030.5691.1737-0.00870.21120.5594-0.01790.13540.35340.04230.6183-53.914811.27951.8151
64.6963-1.45021.59694.20223.16994.10550.8235-1.0253-2.99221.94310.3380.55611.2651-0.7129-1.17681.31780.12190.01111.15270.40721.1101-58.26479.680515.2742
79.0802-3.01591.60559.3581-3.43075.8749-0.8225-1.0725-2.19710.13670.28511.06221.49090.16410.45160.78150.06560.34470.54930.1490.8343-59.916212.5897.4623
85.07926.97974.07732.00564.54085.4545-1.1045-2.83842.49730.98041.37590.6666-1.793-0.5182-0.25650.90590.31480.03720.8086-0.15460.6142-55.284123.626613.0598
95.086-1.8053.54642.6042-2.39893.1514-1.1112-1.45770.88131.79321.5644-0.38780.41242.3298-0.46960.9050.245-0.13660.94930.05580.5844-44.59322.651312.6253
108.77972.2486-1.40125.8099-0.44484.75670.3888-0.02781.8190.12330.397-0.1051-0.43091.3482-0.84880.5488-0.17660.01540.6989-0.08870.7494-17.845229.7258-14.5989
115.12362.5382-0.90974.8747-1.29599.262-0.0503-0.21660.2521-0.18090.61760.060.48290.8625-0.56880.3239-0.0311-0.03040.5387-0.09680.4836-19.088924.0563-13.6723
127.686-2.0846-0.49946.78691.88156.37980.14520.75660.0879-0.52570.15231.47791.2453-1.7865-0.18110.7773-0.4588-0.16231.280.25860.7686-33.690221.1992-22.3072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 215 through 227 )
2X-RAY DIFFRACTION2chain 'A' and (resid 228 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 288 )
5X-RAY DIFFRACTION5chain 'A' and (resid 289 through 312 )
6X-RAY DIFFRACTION6chain 'A' and (resid 313 through 324 )
7X-RAY DIFFRACTION7chain 'A' and (resid 325 through 337 )
8X-RAY DIFFRACTION8chain 'A' and (resid 338 through 344 )
9X-RAY DIFFRACTION9chain 'A' and (resid 345 through 351 )
10X-RAY DIFFRACTION10chain 'B' and (resid 215 through 238 )
11X-RAY DIFFRACTION11chain 'B' and (resid 239 through 295 )
12X-RAY DIFFRACTION12chain 'B' and (resid 296 through 351 )

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