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- PDB-2pvc: DNMT3L recognizes unmethylated histone H3 lysine 4 -

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Basic information

Entry
Database: PDB / ID: 2pvc
TitleDNMT3L recognizes unmethylated histone H3 lysine 4
Components
  • DNA (cytosine-5)-methyltransferase 3-like
  • Histone H3 peptide
KeywordsTransferase regulator / DNMT3L / unmethylated H3K4 / de novo DNA methylation
Function / homology
Function and homology information


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 / 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 ...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 / 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 / DNA metabolic process / male meiosis I / catalytic complex / enzyme activator activity / heterochromatin / DNA methylation / placenta development / condensed nuclear chromosome / stem cell differentiation / methylation / spermatogenesis / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
: / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / ADD domain / ADD domain profile. / Vaccinia Virus protein VP39 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...: / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / ADD domain / ADD domain profile. / 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 / Alpha Beta
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 3-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å
AuthorsCheng, X.
CitationJournal: Nature / Year: 2007
Title: DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.
Authors: Ooi, S.K. / Qiu, C. / Bernstein, E. / Li, K. / Jia, D. / Yang, Z. / Erdjument-Bromage, H. / Tempst, P. / Lin, S.P. / Allis, C.D. / Cheng, X. / Bestor, T.H.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence Author's sequence match to GenBank entry BC002560.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (cytosine-5)-methyltransferase 3-like
D: Histone H3 peptide
A: DNA (cytosine-5)-methyltransferase 3-like
E: Histone H3 peptide
C: DNA (cytosine-5)-methyltransferase 3-like
F: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,51115
Polymers132,9236
Non-polymers5899
Water0
1
B: DNA (cytosine-5)-methyltransferase 3-like
D: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5045
Polymers44,3082
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA (cytosine-5)-methyltransferase 3-like
E: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5045
Polymers44,3082
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (cytosine-5)-methyltransferase 3-like
F: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5045
Polymers44,3082
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)267.7, 267.7, 150.0
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 43530.645 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Plasmid: pET-28a,pXC391 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UJW3
#2: Protein/peptide Histone H3 peptide


Mass: 776.881 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Synthetic Histone H3 peptide
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

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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: 5.89 Å3/Da / Density % sol: 79.13 %
Crystal growTemperature: 300 K / pH: 7.5
Details: 12 % polyethylene glycol, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.69→35 Å / Num. obs: 30684 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.6
Reflection shellResolution: 3.69→3.83 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.8 / % possible all: 89.4

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PV0

2pv0


Resolution: 3.69→34.41 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 6276309.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1512 5 %RANDOM
Rwork0.264 ---
obs0.264 30239 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4 Å2 / ksol: 0.18 e/Å3
Displacement parametersBiso mean: 136.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.13 Å224.8 Å20 Å2
2---4.13 Å20 Å2
3---8.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.56 Å
Luzzati d res low-40 Å
Luzzati sigma a0.42 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 3.69→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8517 0 9 0 8526
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.461.5
X-RAY DIFFRACTIONc_mcangle_it10.642
X-RAY DIFFRACTIONc_scbond_it8.392
X-RAY DIFFRACTIONc_scangle_it12.762.5
LS refinement shellResolution: 3.69→3.83 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 136 4.7 %
Rwork0.312 2751 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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