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Open data
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Basic information
Entry | Database: PDB / ID: 6erh | |||||||||
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Title | Complex of XLF and heterodimer Ku bound to DNA | |||||||||
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![]() | DNA BINDING PROTEIN / DNA repair complex NHEJ | |||||||||
Function / homology | ![]() positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex ...positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / 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 / U3 snoRNA binding / positive regulation of neurogenesis / cellular response to fatty acid / hematopoietic stem cell proliferation / protein localization to chromosome, telomeric region / cellular hyperosmotic salinity response / response to ionizing radiation / telomeric DNA binding / positive regulation of catalytic activity / 2-LTR circle formation / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / T cell differentiation / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / DNA polymerase binding / DNA helicase activity / : / enzyme activator activity / positive regulation of telomere maintenance via telomerase / activation of innate immune response / telomere maintenance / cyclin binding / B cell differentiation / neurogenesis / cellular response to leukemia inhibitory factor / central nervous system development / protein-DNA complex / small-subunit processome / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / fibrillar center / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / scaffold protein binding / double-stranded DNA binding / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / chromosome, telomeric region / damaged DNA binding / transcription cis-regulatory region binding / ribonucleoprotein complex / response to xenobiotic stimulus / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / 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 / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Nemoz, C. / Legrand, P. / Ropars, V. / Charbonnier, J.B. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 974.7 KB | Display | ![]() |
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PDB format | ![]() | 798.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.5 KB | Display | ![]() |
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Full document | ![]() | 547.7 KB | Display | |
Data in XML | ![]() | 71 KB | Display | |
Data in CIF | ![]() | 97 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6erfC ![]() 6ergC ![]() 1jeyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-X-ray repair cross-complementing protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 62629.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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, 4 molecules FOKR
#3: DNA chain | Mass: 10325.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | Mass: 6506.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Protein/peptide , 1 types, 2 molecules MT
#5: Protein/peptide | Mass: 2273.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 2 types, 35 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98015 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.38 Å / Num. obs: 41644 / % possible obs: 50.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 84.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.094 / Rrim(I) all: 0.182 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.8→3.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.6 / Rpim(I) all: 0.76 / Rrim(I) all: 1.47 / % possible all: 8.5 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JEY Resolution: 2.8→49.38 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.572
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Displacement parameters | Biso max: 211.31 Å2 / Biso mean: 87.61 Å2 / Biso min: 3.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.51 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→49.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 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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