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- PDB-2qrv: Structure of Dnmt3a-Dnmt3L C-terminal domain complex -

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Basic information

Entry
Database: PDB / ID: 2qrv
TitleStructure of Dnmt3a-Dnmt3L C-terminal domain complex
Components
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5)-methyltransferase 3A
Keywordstransferase/transferase regulator / DNA methyltransferase 3a (Dnmt3a) and its regulatory factor / DNA methyltransferase 3-like protein (Dnmt3L) / Nucleus / S-adenosyl-L-methionine / transferase-transferase regulator COMPLEX
Function / homology
Function and homology information


retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase ...retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / negative regulation of DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / XY body / cellular response to ethanol / response to vitamin A / negative regulation of gene expression via chromosomal CpG island methylation / DNA metabolic process / negative regulation of gene expression, epigenetic / response to ionizing radiation / hepatocyte apoptotic process / male meiosis I / chromosome, centromeric region / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / PRC2 methylates histones and DNA / response to cocaine / condensed nuclear chromosome / Defective pyroptosis / stem cell differentiation / placenta development / cellular response to amino acid stimulus / response to lead ion / euchromatin / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / transcription corepressor activity / response to estradiol / cellular response to hypoxia / methylation / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #90 / DNA (cytosine-5)-methyltransferase 3A, 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. / Ubiquitin Ligase Nedd4; Chain: W; / DNA methylase, C-5 cytosine-specific, active site ...Ubiquitin Ligase Nedd4; Chain: W; - #90 / DNA (cytosine-5)-methyltransferase 3A, 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. / Ubiquitin Ligase Nedd4; Chain: W; / 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 / Single Sheet / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3-like / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsJia, D. / Cheng, X.
CitationJournal: Nature / Year: 2007
Title: Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.
Authors: Jia, D. / Jurkowska, R.Z. / Zhang, X. / Jeltsch, A. / Cheng, X.
History
DepositionJul 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
E: DNA (cytosine-5)-methyltransferase 3A
F: DNA (cytosine-5)-methyltransferase 3-like
G: DNA (cytosine-5)-methyltransferase 3-like
H: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,15212
Polymers242,6158
Non-polymers1,5384
Water0
1
A: DNA (cytosine-5)-methyltransferase 3A
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0766
Polymers121,3074
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (cytosine-5)-methyltransferase 3A
F: DNA (cytosine-5)-methyltransferase 3-like
G: DNA (cytosine-5)-methyltransferase 3-like
H: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0766
Polymers121,3074
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)401.881, 401.881, 49.689
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThere were two tetramer complexes per crystallographic asymmetric unit. Each tetramer contains two pairs of Dnmt3a-3L hetero-dimers (3L-3a-3a-3L) with two 3L-3a interfaces and one 3a-3a interface.

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Components

#1: Protein
DNA (cytosine-5)-methyltransferase 3A / DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA


Mass: 33961.148 Da / Num. of mol.: 4 / Fragment: residues 623 to 908
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Plasmid: pXC528 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#2: Protein
DNA (cytosine-5)-methyltransferase 3-like


Mass: 26692.486 Da / Num. of mol.: 4 / Fragment: residues 160 to 386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Plasmid: pXC510 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UJW3
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 3.18 Å3/Da / Density % sol: 61.29 %
Description: THERE ARE TWO TETRAMER COMPLEXES PER ASYMMETRIC UNIT. TETRAMER FORMED BY CHAINS A,B,C,D IS MORE STABLE THAN THE TETRAMER FORMED BY CHAINS E,F,G,H. WITHIN EACH TETRAMER, THE DNMT3L ...Description: THERE ARE TWO TETRAMER COMPLEXES PER ASYMMETRIC UNIT. TETRAMER FORMED BY CHAINS A,B,C,D IS MORE STABLE THAN THE TETRAMER FORMED BY CHAINS E,F,G,H. WITHIN EACH TETRAMER, THE DNMT3L MOLECULES HAVE HIGHER B-FACTOR THAN THAT OF DNMT3A, INDICATING DNMT3L MOLECULES - LOCATED IN THE OUTER SURFACES OF TETRAMER - ARE MORE MOBILE.
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: The final protein solution CONTAINED ~100 TO 133 micro M COMPLEX IN 20 milli M TRIS/HCL, PH 8.0, 100 milli M NACL, 5 % GLYCEROL, AND 0.1 % MERCAPTOETHANOL. Crystals were obtained with the ...Details: The final protein solution CONTAINED ~100 TO 133 micro M COMPLEX IN 20 milli M TRIS/HCL, PH 8.0, 100 milli M NACL, 5 % GLYCEROL, AND 0.1 % MERCAPTOETHANOL. Crystals were obtained with the mother liquor containing 2~5 % PEG 3000, 100 mM Tris/HCl, pH 8.0, 5 % glycerol at 16C, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21731
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0, 0.9792, 0.9785,0.9719
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
30.97851
40.97191
ReflectionResolution: 2.89→40 Å / Num. all: 65264 / Num. obs: 65264 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 85.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.8
Reflection shellResolution: 2.89→2.99 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.8 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PV0

2pv0


Resolution: 2.89→38.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 332407.34 / Data cutoff high rms absF: 332407.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: The non-crystallographic symmetry was used as restrains in the CNS refinement, and was released for the side chains at the later cycles to account for different interaction environments of ...Details: The non-crystallographic symmetry was used as restrains in the CNS refinement, and was released for the side chains at the later cycles to account for different interaction environments of crystal packing with each molecule. The group B-factor for each residue was refined at the earlier stage of refinement and the individual B-factor for each atom was refined at the later cycles.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2756 5.1 %RANDOM
Rwork0.259 ---
all0.259 65264 --
obs0.259 54424 81.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.7996 Å2 / ksol: 0.279674 e/Å3
Displacement parametersBiso mean: 101.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.92 Å224.85 Å20 Å2
2--9.92 Å20 Å2
3----19.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.49 Å
Luzzati d res low-40 Å
Luzzati sigma a0.64 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.89→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14557 0 104 0 14661
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it4.841.5
X-RAY DIFFRACTIONc_mcangle_it7.652
X-RAY DIFFRACTIONc_scbond_it6.42
X-RAY DIFFRACTIONc_scangle_it9.072.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.89→2.99 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.46 121 4.8 %
Rwork0.467 2410 -
obs--38 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4sah.parion.top
X-RAY DIFFRACTION5ion.paramsah.top

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