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- PDB-7o45: Crystal structure of ADD domain of the human DNMT3B methyltransferase -

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Basic information

Entry
Database: PDB / ID: 7o45
TitleCrystal structure of ADD domain of the human DNMT3B methyltransferase
ComponentsIsoform 6 of DNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE / Methyltransferase 3B / DNA methylation / DNMT3B
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 ...: / 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 / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like 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, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like 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
BROMIDE ION / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Bonchuk, A.N. / Georgiev, P.G. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10099 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structure of the DNMT3B ADD domain suggests the absence of a DNMT3A-like autoinhibitory mechanism.
Authors: Boyko, K. / Arkova, O. / Nikolaeva, A. / Popov, V.O. / Georgiev, P. / Bonchuk, A.
History
DepositionApr 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
B: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
C: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
D: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,25119
Polymers66,2274
Non-polymers1,02515
Water2,324129
1
A: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
B: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
C: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,49815
Polymers49,6703
Non-polymers82812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7534
Polymers16,5571
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.282, 89.943, 92.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 414 - 554 / Label seq-ID: 6 - 146

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Isoform 6 of DNA (cytosine-5)-methyltransferase 3B / Dnmt3b / DNA methyltransferase HsaIIIB / DNA MTase HsaIIIB / M.HsaIIIB


Mass: 16556.688 Da / Num. of mol.: 4
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaBr; 0.1M bis-tris-propane pH 7.5; 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 1.284 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 2.1→89.94 Å / Num. obs: 36578 / % possible obs: 92.5 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Net I/σ(I): 10.8 / Num. measured all: 129767 / Scaling rejects: 74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.163.10.908775625070.6670.5611.0751.579.3
8.9-89.943.40.02917555230.9630.0190.03528.390.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qbr

4qbr


Resolution: 2.1→64.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.535 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1810 5 %RANDOM
Rwork0.2 ---
obs0.2015 34698 92.05 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 159.67 Å2 / Biso mean: 53.627 Å2 / Biso min: 21.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å2-0 Å2-0 Å2
2--1.66 Å20 Å2
3---0.87 Å2
Refinement stepCycle: final / Resolution: 2.1→64.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 15 129 4041
Biso mean--57.4 45.71 -
Num. residues----507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134036
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183568
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6675427
X-RAY DIFFRACTIONr_angle_other_deg1.2681.5838205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68721.31229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72215661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.571536
X-RAY DIFFRACTIONr_chiral_restr0.0830.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024612
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02996
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41440.12
12B41440.12
21A42280.09
22C42280.09
31B41870.11
32C41870.11
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 113 -
Rwork0.274 2200 -
all-2313 -
obs--80.2 %
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)
11.60640.230.79981.27430.852.20570.143-0.2325-0.17440.1617-0.0321-0.10750.248-0.1531-0.11090.0354-0.0263-0.02550.15040.01210.0594-22.5525-20.526717.3836
22.93491.34930.27012.26920.21380.518-0.12970.5506-0.2514-0.2490.2107-0.20520.06860.1282-0.08090.049-0.0040.02540.2877-0.11810.0997-26.9939-25.2331-12.5965
31.6258-0.121-0.0350.7599-0.48061.74110.02910.20030.22290.0507-0.0252-0.0831-0.16430.1246-0.0040.0274-0.02330.02650.14310.01070.089-10.7718-1.2098-2.9565
48.9225-1.84260.30135.2360.55160.8964-0.1145-0.41981.22640.29510.20320.5345-0.28770.1227-0.08880.1453-0.03970.10320.0524-0.05050.4367-45.9233-1.7524-3.3122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A414 - 554
2X-RAY DIFFRACTION2B414 - 554
3X-RAY DIFFRACTION3C414 - 554
4X-RAY DIFFRACTION4D420 - 550

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