+Open data
-Basic information
Entry | Database: PDB / ID: 7svb | ||||||||||||
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Title | APE1 exonuclease substrate complex with 8oxoG opposite C | ||||||||||||
Components |
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Keywords | HYDROLASE/DNA / nuclease / DNA Repair protein / DNA binding protein / HYDROLASE / HYDROLASE-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) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||||||||
Authors | Whitaker, A.W. / Freudenthal, B.D. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Processing oxidatively damaged bases at DNA strand breaks by APE1. Authors: Whitaker, A.M. / Stark, W.J. / 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 | 7svb.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7svb.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 7svb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7svb_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 7svb_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 7svb_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 7svb_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/7svb ftp://data.pdbj.org/pub/pdb/validation_reports/sv/7svb | HTTPS FTP |
-Related structure data
Related structure data | 7suvC 5dfiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: DNA chain | Mass: 3117.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: DNA chain | Mass: 6409.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#4: Protein | Mass: 31154.504 Da / Num. of mol.: 2 / Mutation: E96Q, C138A, D210N 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 #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: 53.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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 24, 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: 2.24→25 Å / Num. obs: 65243 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.73 Å2 / Rrim(I) all: 0.133 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.24→2.29 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.72 / Num. unique obs: 12091 / Rpim(I) all: 0.658 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dfI Resolution: 2.24→24.76 Å / SU ML: 0.3191 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3016 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→24.76 Å
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Refine LS restraints |
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LS refinement shell |
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