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- PDB-5w7y: Crystal Structure of FHA domain of human APLF in complex with XRC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w7y | ||||||
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Title | Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide | ||||||
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![]() | PROTEIN BINDING / scaffold protein / DNA repair / NHEJ | ||||||
Function / homology | ![]() 3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / positive regulation of DNA ligase activity / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / regulation of isotype switching / histone chaperone activity ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / positive regulation of DNA ligase activity / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / regulation of isotype switching / histone chaperone activity / poly-ADP-D-ribose binding / positive regulation of single strand break repair / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / voluntary musculoskeletal movement / cerebellum morphogenesis / single strand break repair / replication-born double-strand break repair via sister chromatid exchange / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / DNA repair-dependent chromatin remodeling / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / protein folding chaperone / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / embryo implantation / Gap-filling DNA repair synthesis and ligation in GG-NER / : / DNA endonuclease activity / hippocampus development / base-excision repair / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / site of double-strand break / histone binding / chromosome, telomeric region / Hydrolases; Acting on ester bonds / response to hypoxia / response to xenobiotic stimulus / DNA repair / nucleotide binding / DNA damage response / chromatin / nucleolus / enzyme binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pedersen, L.C. / Kim, K. / London, R.E. | ||||||
![]() | ![]() Title: Characterization of the APLF FHA-XRCC1 phosphopeptide interaction and its structural and functional implications. Authors: Kim, K. / Pedersen, L.C. / Kirby, T.W. / DeRose, E.F. / London, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 41.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 439 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w7wC ![]() 5w7xSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11921.815 Da / Num. of mol.: 2 / Fragment: UNP residues 1-105 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8IW19, DNA-(apurinic or apyrimidinic site) lyase #2: Protein/peptide | Mass: 960.833 Da / Num. of mol.: 2 / Fragment: UNP residues 514-521 / Mutation: S518E / Source method: obtained synthetically / Details: XRCC1 S518E mutation pT peptide / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.449 Å / Num. obs: 11773 / % possible obs: 92.3 % / Redundancy: 2.4 % / Rpim(I) all: 0.23 / Rsym value: 0.112 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 486 / Rpim(I) all: 0.23 / Rsym value: 0.316 / % possible all: 87.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W7X Resolution: 2.1→29.449 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 26.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.449 Å
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Refine LS restraints |
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LS refinement shell |
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