+Open data
-Basic information
Entry | Database: PDB / ID: 3pta | ||||||
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Title | Crystal structure of human DNMT1(646-1600) in complex with DNA | ||||||
Components |
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Keywords | Transferase/DNA / DNMT1 / Maintenance DNA methylation / Transferase-DNA complex | ||||||
Function / homology | Function and homology information chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation ...chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / STAT3 nuclear events downstream of ALK signaling / female germ cell nucleus / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / Nuclear events stimulated by ALK signaling in cancer / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / DNA methylation / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / NoRC negatively regulates rRNA expression / methylation / negative regulation of gene expression / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Song, J. / Patel, D.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pta.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pta.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pta_validation.pdf.gz | 746.9 KB | Display | wwPDB validaton report |
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Full document | 3pta_full_validation.pdf.gz | 806.6 KB | Display | |
Data in XML | 3pta_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 3pta_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/3pta ftp://data.pdbj.org/pub/pdb/validation_reports/pt/3pta | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 108060.328 Da / Num. of mol.: 1 / Fragment: UNP residues 646-1600 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT1, AIM, CXXC9, DNMT / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: P26358, DNA (cytosine-5-)-methyltransferase |
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#2: DNA chain | Mass: 5782.724 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 5871.786 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-SAH / |
#5: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.58 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 6% PEG 20,000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2009 |
Radiation | Monochromator: Si mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2827 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→30 Å / Num. all: 19266 / Num. obs: 19075 / % possible obs: 99 % / Observed criterion σ(I): -0.5 / Redundancy: 7.2 % / Rsym value: 0.101 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.508 / % possible all: 94.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→30 Å / σ(F): 0 / Stereochemistry target values: MLF
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Refinement step | Cycle: LAST / Resolution: 3.6→30 Å
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Refine LS restraints |
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