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- PDB-8tci: Crystal structure of DNMT3C-DNMT3L in complex with CGG DNA -

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Basic information

Entry
Database: PDB / ID: 8tci
TitleCrystal structure of DNMT3C-DNMT3L in complex with CGG DNA
Components
  • (5'-D(P*CP*AP*TP*G)-R(P*(PYO))-D(P*GP*GP*TP*CP*TP*AP*AP*TP*TP*AP*GP*AP*CP*CP*GP*CP*AP*TP*G)-3')
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3C
KeywordsTRANSFERASE / DNA cytosine methyltransferase
Function / homology
Function and homology information


: / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / genomic imprinting / homologous chromosome pairing at meiosis / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity ...: / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / genomic imprinting / homologous chromosome pairing at meiosis / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / DNA methylation-dependent heterochromatin formation / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / condensed nuclear chromosome / stem cell differentiation / placenta development / spermatogenesis / methylation / cell differentiation / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytosol
Similarity search - Function
: / 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 ...: / 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 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase 3C / DNA (cytosine-5)-methyltransferase 3-like
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsKhudaverdyan, N. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The structure of DNA methyltransferase DNMT3C reveals an activity-tuning mechanism for DNA methylation.
Authors: Khudaverdyan, N. / Lu, J. / Chen, X. / Herle, G. / Song, J.
History
DepositionJul 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3C
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3C
E: (5'-D(P*CP*AP*TP*G)-R(P*(PYO))-D(P*GP*GP*TP*CP*TP*AP*AP*TP*TP*AP*GP*AP*CP*CP*GP*CP*AP*TP*G)-3')
F: (5'-D(P*CP*AP*TP*G)-R(P*(PYO))-D(P*GP*GP*TP*CP*TP*AP*AP*TP*TP*AP*GP*AP*CP*CP*GP*CP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6308
Polymers125,8616
Non-polymers7692
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13020 Å2
ΔGint-54 kcal/mol
Surface area46490 Å2
Unit cell
Length a, b, c (Å)63.088, 189.509, 62.864
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3C / Dnmt3c


Mass: 32535.496 Da / Num. of mol.: 2 / Fragment: UNP residues 458-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt3c, Gm14490 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DOY1, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 23024.424 Da / Num. of mol.: 2 / Fragment: UNP residues 181-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UJW3
#3: DNA chain (5'-D(P*CP*AP*TP*G)-R(P*(PYO))-D(P*GP*GP*TP*CP*TP*AP*AP*TP*TP*AP*GP*AP*CP*CP*GP*CP*AP*TP*G)-3')


Mass: 7370.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2% v/v Tacsimate, pH 8.0, 0.1 M Tris, pH 8.5, 16% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 23776 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.93 / CC star: 0.982 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.118 / Rrim(I) all: 0.224 / Χ2: 5.874 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.2-3.313.30.99923870.5490.8420.6451.1921.36299.5
3.31-3.453.30.72423630.6430.8850.4650.8621.53499.7
3.45-3.63.30.53123560.7310.9190.3370.6311.8799.4
3.6-3.793.30.38723680.8390.9550.2460.462.27499.4
3.79-4.033.30.32423740.8890.970.2050.3852.95799.4
4.03-4.343.40.24723490.9250.980.1540.2914.65799.1
4.34-4.783.40.21123810.940.9840.1310.2497.53699.1
4.78-5.473.50.17823630.950.9870.110.216.61799.1
5.47-6.893.70.14124110.9760.9940.0850.1656.24199.9
6.89-503.80.09824240.9710.9930.0590.11420.434100

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6U8P

6u8p


Resolution: 3.19→44.56 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 2021 8.53 %
Rwork0.2248 --
obs0.2277 23704 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7382 984 52 0 8418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038747
X-RAY DIFFRACTIONf_angle_d0.56212102
X-RAY DIFFRACTIONf_dihedral_angle_d18.9053302
X-RAY DIFFRACTIONf_chiral_restr0.041336
X-RAY DIFFRACTIONf_plane_restr0.0051398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.270.3405900.34021019X-RAY DIFFRACTION63
3.27-3.360.36781430.30531561X-RAY DIFFRACTION99
3.36-3.460.30071540.30031590X-RAY DIFFRACTION100
3.46-3.570.28911480.27521610X-RAY DIFFRACTION99
3.57-3.70.30221490.26331605X-RAY DIFFRACTION100
3.7-3.850.29531440.25291548X-RAY DIFFRACTION99
3.85-4.020.29571480.24611580X-RAY DIFFRACTION99
4.02-4.230.24431600.22831609X-RAY DIFFRACTION99
4.23-4.50.24051530.19821574X-RAY DIFFRACTION99
4.5-4.840.2361390.19151615X-RAY DIFFRACTION99
4.84-5.330.23531450.20561534X-RAY DIFFRACTION99
5.33-6.10.24191470.22551606X-RAY DIFFRACTION100
6.1-7.670.23791560.21721614X-RAY DIFFRACTION100
7.69-44.560.21941450.1841618X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.3682 Å / Origin y: -2.9605 Å / Origin z: 15.6081 Å
111213212223313233
T0.5137 Å20.0032 Å20.0135 Å2-0.5447 Å20.0051 Å2--0.4954 Å2
L0.0874 °20.0482 °20.018 °2-2.7803 °22.02 °2--1.553 °2
S0.0114 Å °-0.0063 Å °0.0182 Å °-0.0052 Å °-0.2488 Å °0.3707 Å °-0.0194 Å °-0.2366 Å °0.2271 Å °
Refinement TLS groupSelection details: all

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