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Yorodumi- PDB-1de8: HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1de8 | ||||||
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Title | HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA | ||||||
Components |
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Keywords | LYASE/DNA / ENZYME:DNA COMPLEX / DNA REPAIR / ABASIC SITE / LYASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / chromosome, telomeric region / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å | ||||||
Authors | Mol, C.D. / Izumi, T. / Mitra, S. / Tainer, J.A. | ||||||
Citation | Journal: Nature / Year: 2000 Title: DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected Authors: Mol, C.D. / Izumi, T. / Mitra, S. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1de8.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1de8.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 1de8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1de8_validation.pdf.gz | 394.6 KB | Display | wwPDB validaton report |
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Full document | 1de8_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 1de8_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1de8_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1de8 ftp://data.pdbj.org/pub/pdb/validation_reports/de/1de8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3225.100 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3374.210 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 31198.559 Da / Num. of mol.: 2 / Fragment: APE1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) Keywords: DNA CONTAINS TETRAHYDROFURAN ABASIC SITE ANALOG 3DR References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase #4: 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: 2.65 Å3/Da / Density % sol: 53.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPEG 5000, LITHIUM SULFATE, MES BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS 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: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 19, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→20 Å / Num. obs: 15572 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.7 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.302 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 42400 |
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
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Refinement | Resolution: 2.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER Details: OVERALL ANISOTROPIC AND BULK-SOLVENT CORRECTIONS APPLIED TO NATIVE DATA SET
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Refinement step | Cycle: LAST / Resolution: 2.95→20 Å
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Refine LS restraints |
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