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- PDB-7v0e: Crystal structure of the macro-oligomeric form of DNMT3B methyltr... -

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Basic information

Entry
Database: PDB / ID: 7v0e
TitleCrystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain.
ComponentsDNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE / DNMT3B / DNA methylation / Methyltransferase
Function / homology
Function and homology information


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 ...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
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27016388184 Å
AuthorsGao, L. / Lu, J. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure of DNMT3B homo-oligomer reveals vulnerability to impairment by ICF mutations.
Authors: Gao, L. / Guo, Y. / Biswal, M. / Lu, J. / Yin, J. / Fang, J. / Chen, X. / Shao, Z. / Huang, M. / Wang, Y. / Wang, G.G. / Song, J.
History
DepositionMay 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: 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
Revision 1.2Oct 18, 2023Group: 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 3B
B: DNA (cytosine-5)-methyltransferase 3B
C: DNA (cytosine-5)-methyltransferase 3B
D: DNA (cytosine-5)-methyltransferase 3B
E: DNA (cytosine-5)-methyltransferase 3B
F: DNA (cytosine-5)-methyltransferase 3B
G: DNA (cytosine-5)-methyltransferase 3B
H: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,32816
Polymers260,2538
Non-polymers3,0758
Water52229
1
A: DNA (cytosine-5)-methyltransferase 3B
D: DNA (cytosine-5)-methyltransferase 3B
E: DNA (cytosine-5)-methyltransferase 3B
F: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6648
Polymers130,1274
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 3B
C: DNA (cytosine-5)-methyltransferase 3B
G: DNA (cytosine-5)-methyltransferase 3B
H: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6648
Polymers130,1274
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.393, 164.393, 209.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

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


Mass: 32531.625 Da / Num. of mol.: 8
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: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 6.52 Å3/Da / Density % sol: 81.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH6.5, 1.4 M Ammonium sulfate, 0.2 mM AdoHcy and 8% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9195 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 3.27→142.37 Å / Num. obs: 93113 / % possible obs: 95.3 % / Redundancy: 3 % / Biso Wilson estimate: 77.616004121 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.2
Reflection shellResolution: 3.27→3.33 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4439 / CC1/2: 0.36 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U8P

6u8p


Resolution: 3.27016388184→84.2879255551 Å / SU ML: 0.442274794998 / Cross valid method: FREE R-VALUE / σ(F): 1.96362416394 / Phase error: 24.7193021628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234582384558 2021 2.17101729509 %
Rwork0.205608383487 91069 -
obs0.206233223941 93090 95.2639227164 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7766686248 Å2
Refinement stepCycle: LAST / Resolution: 3.27016388184→84.2879255551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17217 0 0 29 17246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071255778008417640
X-RAY DIFFRACTIONf_angle_d0.86834608048623876
X-RAY DIFFRACTIONf_chiral_restr0.05273399624532600
X-RAY DIFFRACTIONf_plane_restr0.00525328658263040
X-RAY DIFFRACTIONf_dihedral_angle_d20.1074117726458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2702-3.35190.3966561853311310.3407121226686132X-RAY DIFFRACTION89.30557536
3.3519-3.44260.3435880102261560.3089995920566557X-RAY DIFFRACTION97.1209490741
3.4426-3.54390.3556473354071470.2776469405196650X-RAY DIFFRACTION96.9614835949
3.5439-3.65830.2741617892281430.2401908510836647X-RAY DIFFRACTION97.0970970971
3.6583-3.7890.2767251009971500.2371683465286556X-RAY DIFFRACTION96.5864899899
3.789-3.94070.2475528352211380.2149154235896586X-RAY DIFFRACTION96.3185790001
3.9407-4.12010.2541189606291450.1968075899696324X-RAY DIFFRACTION92.2298260622
4.1201-4.33730.2175925132091470.173002163596564X-RAY DIFFRACTION96.658504969
4.3373-4.6090.1825392274141430.1564353256356692X-RAY DIFFRACTION98.1194372667
4.609-4.96480.2044238277431450.1619945124156683X-RAY DIFFRACTION97.4593205824
4.9648-5.46440.2106059510061500.1779280917376268X-RAY DIFFRACTION91.7774917775
5.4644-6.25490.2109216401581460.2109216401586649X-RAY DIFFRACTION97.7838537919
6.2549-7.87960.2085984134361460.2140204613046518X-RAY DIFFRACTION95.118469883
7.8796-84.28792555510.193354051071340.1888512542626243X-RAY DIFFRACTION91.4527463072

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