+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12301 | |||||||||
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Title | Cryo-EM structure of NHEJ super-complex (monomer) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NHEJ / DNA-PKcs / Ku70/80 / XLF / XRCC4 / DNA-LigaseIV / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation ...DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation / positive regulation of platelet formation / DNA ligase (ATP) / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / cellular response to X-ray / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / regulation of smooth muscle cell proliferation / V(D)J recombination / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / isotype switching / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / regulation of epithelial cell proliferation / IRF3-mediated induction of type I IFN / telomere capping / recombinational repair / regulation of hematopoietic stem cell differentiation / regulation of telomere maintenance / U3 snoRNA binding / protein localization to chromosome, telomeric region / cellular response to fatty acid / nucleotide-excision repair, DNA gap filling / positive regulation of neurogenesis / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / positive regulation of catalytic activity / condensed chromosome / T cell lineage commitment / negative regulation of cGAS/STING signaling pathway / response to ionizing radiation / telomeric DNA binding / DNA biosynthetic process / cellular response to lithium ion / double-strand break repair via alternative nonhomologous end joining / maturation of 5.8S rRNA / B cell lineage commitment / 2-LTR circle formation / positive regulation of double-strand break repair via nonhomologous end joining / mitotic G1 DNA damage checkpoint signaling / ligase activity / : / site of DNA damage / somatic stem cell population maintenance / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / cyclin binding / T cell differentiation / response to X-ray / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / chromosome organization / positive regulation of protein kinase activity / ectopic germ cell programmed cell death / ATP-dependent activity, acting on DNA / neurogenesis / somitogenesis / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / enzyme activator activity / positive regulation of telomere maintenance via telomerase / activation of innate immune response / DNA helicase activity / telomere maintenance / B cell differentiation / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / stem cell proliferation / cellular response to leukemia inhibitory factor / Nonhomologous End-Joining (NHEJ) / central nervous system development / small-subunit processome / positive regulation of translation / regulation of circadian rhythm / cellular response to ionizing radiation / protein-DNA complex / response to gamma radiation / peptidyl-threonine phosphorylation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.29 Å | |||||||||
Authors | Chaplin AK / Hardwick SW | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Cryo-EM of NHEJ supercomplexes provides insights into DNA repair. Authors: Amanda K Chaplin / Steven W Hardwick / Antonia Kefala Stavridi / Christopher J Buehl / Noah J Goff / Virginie Ropars / Shikang Liang / Taiana Maia De Oliveira / Dimitri Y Chirgadze / ...Authors: Amanda K Chaplin / Steven W Hardwick / Antonia Kefala Stavridi / Christopher J Buehl / Noah J Goff / Virginie Ropars / Shikang Liang / Taiana Maia De Oliveira / Dimitri Y Chirgadze / Katheryn Meek / Jean-Baptiste Charbonnier / Tom L Blundell / Abstract: Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or ...Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or cancer. NHEJ involves several proteins, including the Ku70/80 heterodimer, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and ligase IV. These core proteins bind DSBs and ligate the damaged DNA ends. However, details of the structural assembly of these proteins remain unclear. Here, we present cryo-EM structures of NHEJ supercomplexes that are composed of these core proteins and DNA, revealing the detailed structural architecture of this assembly. We describe monomeric and dimeric forms of this supercomplex and also propose the existence of alternate dimeric forms of long-range synaptic complexes. Finally, we show that mutational disruption of several structural features within these NHEJ complexes negatively affects DNA repair. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12301.map.gz | 557.6 MB | EMDB map data format | |
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Header (meta data) | emd-12301-v30.xml emd-12301.xml | 31.4 KB 31.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12301_fsc.xml | 18.8 KB | Display | FSC data file |
Images | emd_12301.png | 57.1 KB | ||
Filedesc metadata | emd-12301.cif.gz | 10.9 KB | ||
Others | emd_12301_half_map_1.map.gz emd_12301_half_map_2.map.gz | 556.7 MB 556.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12301 | HTTPS FTP |
-Validation report
Summary document | emd_12301_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_12301_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_12301_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | emd_12301_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12301 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12301 | HTTPS FTP |
-Related structure data
Related structure data | 7nfeMC 7nfcC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12301.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.304 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_12301_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12301_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : NHEJ super-complex (monomer)
+Supramolecule #1: NHEJ super-complex (monomer)
+Supramolecule #2: DNA-dependent protein kinase catalytic subunit
+Supramolecule #3: X-ray repair cross-complementing protein 6 and 5
+Supramolecule #4: Non-homologous end-joining factor 1,DNA repair protein XRCC4, DNA...
+Supramolecule #5: DNA
+Macromolecule #1: DNA-dependent protein kinase catalytic subunit,DNA-dependent prot...
+Macromolecule #2: X-ray repair cross-complementing protein 6
+Macromolecule #3: X-ray repair cross-complementing protein 5
+Macromolecule #4: Non-homologous end-joining factor 1
+Macromolecule #5: DNA repair protein XRCC4
+Macromolecule #6: DNA ligase 4
+Macromolecule #7: DNA (5'-D(P*AP*AP*TP*AP*AP*AP*CP*TP*AP*AP*AP*AP*AP*CP*TP*AP*TP*TP...
+Macromolecule #8: DNA (5'-D(P*TP*AP*AP*TP*AP*AP*TP*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.3 sec. / Average electron dose: 46.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |