+Open data
-Basic information
Entry | Database: PDB / ID: 6erf | ||||||||||||
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Title | Complex of APLF factor and Ku heterodimer bound to DNA | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA repair protein NHEJ | ||||||||||||
Function / homology | Function and homology information ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / Ku70:Ku80 complex / poly-ADP-D-ribose binding / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / positive regulation of DNA ligation ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / Ku70:Ku80 complex / poly-ADP-D-ribose binding / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / DNA repair-dependent chromatin remodeling / U3 snoRNA binding / positive regulation of neurogenesis / protein localization to chromosome, telomeric region / cellular response to fatty acid / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / telomeric DNA binding / positive regulation of catalytic activity / 2-LTR circle formation / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / enzyme activator activity / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / protein folding chaperone / embryo implantation / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of telomerase activity / protein localization to chromatin / 3'-5' exonuclease activity / positive regulation of telomere maintenance via telomerase / DNA helicase activity / telomere maintenance / activation of innate immune response / cellular response to leukemia inhibitory factor / small-subunit processome / neurogenesis / cyclin binding / DNA endonuclease activity / protein-DNA complex / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / histone binding / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / damaged DNA binding / chromosome, telomeric region / Hydrolases; Acting on ester bonds / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex / nucleotide binding / DNA repair / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01 Å | ||||||||||||
Authors | Nemoz, C. / Legrand, P. / Ropars, V. / Charbonnier, J.B. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2018 Title: XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Authors: Nemoz, C. / Ropars, V. / Frit, P. / Gontier, A. / Drevet, P. / Yu, J. / Guerois, R. / Pitois, A. / Comte, A. / Delteil, C. / Barboule, N. / Legrand, P. / Baconnais, S. / Yin, Y. / Tadi, S. / ...Authors: Nemoz, C. / Ropars, V. / Frit, P. / Gontier, A. / Drevet, P. / Yu, J. / Guerois, R. / Pitois, A. / Comte, A. / Delteil, C. / Barboule, N. / Legrand, P. / Baconnais, S. / Yin, Y. / Tadi, S. / Barbet-Massin, E. / Berger, I. / Le Cam, E. / Modesti, M. / Rothenberg, E. / Calsou, P. / Charbonnier, J.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6erf.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6erf.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6erf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/6erf ftp://data.pdbj.org/pub/pdb/validation_reports/er/6erf | HTTPS FTP |
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-Related structure data
Related structure data | 6ergC 6erhC 1jeyS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-X-ray repair cross-complementing protein ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 62629.629 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P12956, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases #2: Protein | Mass: 65356.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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-DNA chain , 2 types, 8 molecules IKMOJLNP
#3: DNA chain | Mass: 6506.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | Mass: 10325.685 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Protein/peptide / Non-polymers , 2 types, 12 molecules QRST
#5: Protein/peptide | Mass: 2225.740 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q8IW19, DNA-(apurinic or apyrimidinic site) lyase #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: 3.26 Å3/Da / Density % sol: 62.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.01→49.47 Å / Num. obs: 90993 / % possible obs: 61.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 123 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.051 / Rrim(I) all: 0.072 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3.01→3.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.6 / Rpim(I) all: 0.66 / Rrim(I) all: 0.93 / % possible all: 14.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JEY Resolution: 3.01→49.47 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.474
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Displacement parameters | Biso max: 263.38 Å2 / Biso mean: 121.75 Å2 / Biso min: 44.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.47 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.01→49.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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