+Open data
-Basic information
Entry | Database: PDB / ID: 5wn4 | ||||||
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Title | APE1 exonuclease substrate complex with a C/T mismatch | ||||||
Components |
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Keywords | HYDROLASE / LYASE/DNA / 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 / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I 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 / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I 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 / endonuclease activity / DNA recombination / regulation of apoptotic process / damaged DNA binding / chromosome, telomeric region / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Freudenthal, B.D. / Whitaker, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Molecular snapshots of APE1 proofreading mismatches and removing DNA damage. Authors: Whitaker, A.M. / Flynn, T.S. / Freudenthal, B.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wn4.cif.gz | 154 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wn4.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/5wn4 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/5wn4 | HTTPS FTP |
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-Related structure data
Related structure data | 5wn0C 5wn1C 5wn2C 5wn3C 5wn5C 5dffS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
-DNA chain , 3 types, 3 molecules CDE
#1: DNA chain | Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3077.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 6424.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 2 molecules AB
#4: Protein | Mass: 31156.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1 / Production host: Escherichia coli (E. coli) References: UniProt: P27695, Hydrolases; Acting on ester bonds, DNA-(apurinic or apyrimidinic site) lyase |
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-Non-polymers , 5 types, 189 molecules
#5: Chemical | #6: Chemical | ChemComp-CA / | #7: Chemical | #8: Chemical | ChemComp-CL / | #9: 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: 2.61 Å3/Da / Density % sol: 52.8 % / Mosaicity: 1.37 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 71157 / % possible obs: 95.1 % / Redundancy: 4 % / Biso Wilson estimate: 41.67 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.703 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5DFF Resolution: 2.1→24.56 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.56 Å
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Refine LS restraints |
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LS refinement shell |
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