Protein or peptide: X-ray repair cross-complementing protein 6
Protein or peptide: X-ray repair cross-complementing protein 5
Keywords
NHEJ / Ku70/80 / XRCC5 / XRCC6 / DNA damage / DNA BINDING PROTEIN
Function / homology
Function and homology information
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 / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray ...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 / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / regulation of telomere maintenance / recombinational repair / U3 snoRNA binding / cellular hyperosmotic salinity response / protein localization to chromosome, telomeric region / telomeric DNA binding / 2-LTR circle formation / hematopoietic stem cell proliferation / positive regulation of protein kinase activity / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / neurogenesis / telomere maintenance / DNA helicase activity / activation of innate immune response / cyclin binding / cellular response to leukemia inhibitory factor / Nonhomologous End-Joining (NHEJ) / small-subunit processome / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / double-strand break repair / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / ficolin-1-rich granule lumen / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / protein-containing complex binding / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol Similarity search - Function
Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta ...Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily Similarity search - Domain/homology
X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 3.2 Å
Journal: FEBS J / Year: 2021 Title: SAP domain forms a flexible part of DNA aperture in Ku70/80. Authors: Aleš Hnízda / Petr Tesina / Thanh-Binh Nguyen / Zdeněk Kukačka / Lukas Kater / Amanda K Chaplin / Roland Beckmann / David B Ascher / Petr Novák / Tom L Blundell / Abstract: Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double-strand DNA breaks to maintain genomic integrity during the entire cell cycle. The Ku70/80 complex recognizes DNA ...Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double-strand DNA breaks to maintain genomic integrity during the entire cell cycle. The Ku70/80 complex recognizes DNA breaks and serves as an essential hub for recruitment of NHEJ components. Here, we describe intramolecular interactions of the Ku70 C-terminal domain, known as the SAP domain. Using single-particle cryo-electron microscopy, mass spectrometric analysis of intermolecular cross-linking and molecular modelling simulations, we captured variable positions of the SAP domain depending on DNA binding. The first position was localized at the DNA aperture in the Ku70/80 apo form but was not observed in the DNA-bound state. The second position, which was observed in both apo and DNA-bound states, was found below the DNA aperture, close to the helical arm of Ku70. The localization of the SAP domain in the DNA aperture suggests a function as a flexible entry gate for broken DNA. DATABASES: EM maps have been deposited in EMDB (EMD-11933). Coordinates have been deposited in Protein Data Bank (PDB 7AXZ). Other data are available from corresponding authors upon a request.
History
Deposition
Nov 10, 2020
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Header (metadata) release
Feb 10, 2021
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Map release
Feb 10, 2021
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Update
Jul 9, 2025
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Current status
Jul 9, 2025
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Macromolecule #1: X-ray repair cross-complementing protein 6
Macromolecule
Name: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
UniProtKB: X-ray repair cross-complementing protein 6
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Macromolecule #2: X-ray repair cross-complementing protein 5
Macromolecule
Name: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
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