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- PDB-3pt9: Crystal structure of mouse DNMT1(731-1602) in the free state -

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Basic information

Entry
Database: PDB / ID: 3pt9
TitleCrystal structure of mouse DNMT1(731-1602) in the free state
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / Maintenance DNA methylation
Function / homology
Function and homology information


SUMOylation of DNA methylation proteins / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase ...SUMOylation of DNA methylation proteins / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / S-adenosylmethionine metabolic process / DNA methylation-dependent heterochromatin formation / female germ cell nucleus / methyl-CpG binding / lncRNA binding / negative regulation of gene expression via chromosomal CpG island methylation / germ cell nucleus / heterochromatin / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / replication fork / methyltransferase activity / promoter-specific chromatin binding / nuclear estrogen receptor binding / cellular response to amino acid stimulus / histone deacetylase binding / regulation of cell population proliferation / methylation / regulation of gene expression / response to xenobiotic stimulus / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Bromo adjacent homology (BAH) domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DNA Methylase, subunit A, domain 2 / DMAP1-binding domain / DMAP1-binding domain profile. / DNA Methylase; Chain A, domain 2 ...Bromo adjacent homology (BAH) domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DNA Methylase, subunit A, domain 2 / DMAP1-binding domain / DMAP1-binding domain profile. / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Vaccinia Virus protein VP39 / SH3 type barrels. / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSong, J. / Patel, D.J.
CitationJournal: Science / Year: 2011
Title: Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
Authors: Song, J. / Rechkoblit, O. / Bestor, T.H. / Patel, D.J.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4964
Polymers98,9811
Non-polymers5153
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.567, 79.685, 162.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / Met-1 / DNA methyltransferase MmuI / DNA MTase MmuI / M.MmuI / MCMT


Mass: 98980.555 Da / Num. of mol.: 1 / Fragment: UNP residues 731-1602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL(DE3)
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3,350, 0.2M Lithium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 34630 / Num. obs: 34594 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Rsym value: 0.132
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 3391 / Rsym value: 0.512 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.879 Å / SU ML: 0.33 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1700 5.06 %RANDOM
Rwork0.196 ---
obs0.1991 33580 96.84 %-
all-34630 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.215 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9256 Å20 Å2-0 Å2
2--12.1362 Å2-0 Å2
3----8.2106 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 28 327 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056680
X-RAY DIFFRACTIONf_angle_d0.9519076
X-RAY DIFFRACTIONf_dihedral_angle_d15.6362443
X-RAY DIFFRACTIONf_chiral_restr0.061962
X-RAY DIFFRACTIONf_plane_restr0.0041190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.59050.3291600.24692887X-RAY DIFFRACTION89
2.5905-2.69420.33491750.24733013X-RAY DIFFRACTION94
2.6942-2.81670.30061450.22933137X-RAY DIFFRACTION95
2.8167-2.96510.33261450.21843153X-RAY DIFFRACTION96
2.9651-3.15070.26521940.22383176X-RAY DIFFRACTION98
3.1507-3.39360.28221790.20413182X-RAY DIFFRACTION98
3.3936-3.73450.25851660.20273259X-RAY DIFFRACTION99
3.7345-4.27360.25091630.16673297X-RAY DIFFRACTION99
4.2736-5.37920.18011890.15483303X-RAY DIFFRACTION99
5.3792-29.88120.23651840.19373473X-RAY DIFFRACTION100

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