+Open data
-Basic information
Entry | Database: PDB / ID: 1wyw | ||||||
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Title | Crystal Structure of SUMO1-conjugated thymine DNA glycosylase | ||||||
Components |
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Keywords | HYDROLASE | ||||||
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 / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel 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 / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / base-excision repair, AP site formation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / depyrimidination / negative regulation of action potential / DNA N-glycosylase activity / sodium ion binding / SUMO binding / mismatched DNA binding / small protein activating enzyme binding / Displacement of DNA glycosylase by APEX1 / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / Maturation of nucleoprotein / uracil DNA N-glycosylase activity / DNA demethylation / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / chloride ion binding / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / regulation of embryonic development / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / cellular response to cadmium ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / SUMOylation of chromatin organization proteins / protein kinase C binding / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / transcription coregulator activity / base-excision repair / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Formation of Incision Complex in GG-NER / : / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / double-stranded DNA binding / nuclear membrane / DNA-binding transcription factor binding / damaged DNA binding / nucleic acid binding / protein stabilization / nuclear body / nuclear speck / protein domain specific binding / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / negative regulation of transcription by RNA polymerase II / enzyme binding / magnesium ion binding / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Baba, D. / Maita, N. / Jee, J.G. / Uchimura, Y. / Saitoh, H. / Sugasawa, K. / Hanaoka, F. / Tochio, H. / Hiroaki, H. / Shirakawa, M. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Authors: Baba, D. / Maita, N. / Jee, J.G. / Uchimura, Y. / Saitoh, H. / Sugasawa, K. / Hanaoka, F. / Tochio, H. / Hiroaki, H. / Shirakawa, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wyw.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wyw.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/1wyw ftp://data.pdbj.org/pub/pdb/validation_reports/wy/1wyw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 26177.049 Da / Num. of mol.: 1 / Fragment: central region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q13569, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: Protein | Mass: 11149.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT-E1E2S1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63165 |
-Non-polymers , 4 types, 177 molecules
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.06 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG3350, 0.1M Tris, 0.2M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 19228 / Num. obs: 19228 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / Num. unique all: 53244 / Rsym value: 0.31 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 100 % |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MUG, 1EUV Resolution: 2.1→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.309 / Rfactor Rwork: 0.219 |