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- PDB-2pv0: DNA methyltransferase 3 like protein (DNMT3L) -

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Basic information

Entry
Database: PDB / ID: 2pv0
TitleDNA methyltransferase 3 like protein (DNMT3L)
ComponentsDNA (cytosine-5)-methyltransferase 3-like
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 / DNA methylation-dependent heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex ...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 / DNA methylation-dependent heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / : / male meiosis I / catalytic complex / enzyme activator activity / heterochromatin / DNA methylation / placenta development / condensed nuclear chromosome / stem cell differentiation / spermatogenesis / negative regulation of DNA-templated transcription / 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 / MAD / Resolution: 3.3 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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
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
A: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,18112
Polymers130,5923
Non-polymers5899
Water0
1
A: DNA (cytosine-5)-methyltransferase 3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7274
Polymers43,5311
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7274
Polymers43,5311
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (cytosine-5)-methyltransferase 3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7274
Polymers43,5311
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)267.200, 267.200, 149.500
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: 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: 4

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
15.8948479.134293
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
3001vapor diffusion, hanging drop90.4-0.6 M sodium citrate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
3002vapor diffusion, hanging drop7.512% polyethylene 3350, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0,1.2199,1.2815,1.2826,1.2830
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.21991
31.28151
41.28261
51.2831
ReflectionResolution: 3.29→35 Å / Num. obs: 47346 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.4
Reflection shellResolution: 3.29→3.41 Å / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SnBphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.3→29.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3964301.47 / 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
Rfree0.272 2344 5 %RANDOM
Rwork0.248 ---
obs0.248 46954 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9288 Å2 / ksol: 0.221639 e/Å3
Displacement parametersBiso mean: 114 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å215.28 Å20 Å2
2--2.13 Å20 Å2
3----4.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.47 Å
Luzzati d res low-40 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7852 0 9 0 7861
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_deg1.5
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_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.331.5
X-RAY DIFFRACTIONc_mcangle_it10.362
X-RAY DIFFRACTIONc_scbond_it8.832
X-RAY DIFFRACTIONc_scangle_it12.742.5
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.403 220 4.8 %
Rwork0.375 4404 -
obs--99.2 %
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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