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Yorodumi- PDB-4fnc: Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fnc | ||||||
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Title | Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU) | ||||||
Components |
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Keywords | HYDROLASE/DNA / base excision repair / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / : / sodium ion binding / DNA N-glycosylase activity ...G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / : / sodium ion binding / DNA N-glycosylase activity / mismatched DNA binding / SUMO binding / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / chloride ion binding / regulation of embryonic development / SUMOylation of DNA damage response and repair proteins / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / transcription coregulator activity / epigenetic regulation of gene expression / protein kinase C binding / base-excision repair / PML body / double-stranded DNA binding / DNA-binding transcription factor binding / nucleic acid binding / damaged DNA binding / protein domain specific binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å | ||||||
Authors | Hashimoto, H. / Hong, S. / Bhagwat, A.S. / Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation. Authors: Hashimoto, H. / Hong, S. / Bhagwat, A.S. / Zhang, X. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fnc.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fnc.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fnc_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 4fnc_full_validation.pdf.gz | 463.9 KB | Display | |
Data in XML | 4fnc_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4fnc_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/4fnc ftp://data.pdbj.org/pub/pdb/validation_reports/fn/4fnc | HTTPS FTP |
-Related structure data
Related structure data | 2rbaS S: Starting model for refinement |
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Similar 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: 23070.670 Da / Num. of mol.: 1 Fragment: human TDG glycosylase domain, UNP residues 111-308 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDG / Plasmid: pXC1056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13569, thymine-DNA glycosylase |
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#2: DNA chain | Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis |
#3: DNA chain | Mass: 8777.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis |
#4: Chemical | ChemComp-HMU / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% polyethylene glycol (PEG) 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2011 Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing, Rosenbaum-Rock vertical focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→39.161 Å / Num. obs: 13702 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 58.71 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1282 / % possible all: 93.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RBA Resolution: 2.493→39.161 Å / SU ML: 0.86 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.807 Å2 / ksol: 0.321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.493→39.161 Å
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Refine LS restraints |
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LS refinement shell |
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