+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16145 | |||||||||
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Title | Cryo-EM structure of NHEJ supercomplex(trimer) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NHEJ / DNA-PK / DNA-PKcs / Ku70 / Ku80 / XLF / DNA repair / 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 / double-strand break repair via classical nonhomologous end joining / isotype switching / 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 telomere maintenance / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / positive regulation of neurogenesis / cellular response to fatty acid / nucleotide-excision repair, DNA gap filling / hematopoietic stem cell proliferation / protein localization to chromosome, telomeric region / cellular hyperosmotic salinity response / T cell lineage commitment / response to ionizing radiation / negative regulation of cGAS/STING signaling pathway / DNA biosynthetic process / cellular response to lithium ion / telomeric DNA binding / maturation of 5.8S rRNA / positive regulation of catalytic activity / B cell lineage commitment / double-strand break repair via alternative nonhomologous end joining / 2-LTR circle formation / positive regulation of double-strand break repair via nonhomologous end joining / ligase activity / site of DNA damage / somatic stem cell population maintenance / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 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 / somitogenesis / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / condensed chromosome / DNA helicase activity / positive regulation of telomerase activity / enzyme activator activity / mitotic G1 DNA damage checkpoint signaling / positive regulation of telomere maintenance via telomerase / activation of innate immune response / telomere maintenance / cyclin binding / B cell differentiation / neurogenesis / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / stem cell proliferation / cellular response to leukemia inhibitory factor / central nervous system development / positive regulation of translation / cellular response to ionizing radiation / response to gamma radiation / protein-DNA complex / Nonhomologous End-Joining (NHEJ) / small-subunit processome / peptidyl-threonine phosphorylation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.76 Å | |||||||||
Authors | Hardwick SW / Chaplin AK | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Structure / Year: 2023 Title: Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ. Authors: Steven W Hardwick / Antonia Kefala Stavridi / Dimitri Y Chirgadze / Taiana Maia De Oliveira / Jean-Baptiste Charbonnier / Virginie Ropars / Katheryn Meek / Tom L Blundell / Amanda K Chaplin / Abstract: The ability of humans to maintain the integrity of the genome is imperative for cellular survival. DNA double-strand breaks (DSBs) are considered the most critical type of DNA lesion, which can ...The ability of humans to maintain the integrity of the genome is imperative for cellular survival. DNA double-strand breaks (DSBs) are considered the most critical type of DNA lesion, which can ultimately lead to diseases including cancer. Non-homologous end joining (NHEJ) is one of two core mechanisms utilized to repair DSBs. DNA-PK is a key component in this process and has recently been shown to form alternate long-range synaptic dimers. This has led to the proposal that these complexes can be formed before transitioning to a short-range synaptic complex. Here we present cryo-EM data representing an NHEJ supercomplex consisting of a trimer of DNA-PK in complex with XLF, XRCC4, and DNA Ligase IV. This trimer represents a complex of both long-range synaptic dimers. We discuss the potential role of the trimeric structure, and possible higher order oligomers, as structural intermediates in the NHEJ mechanism, or as functional DNA repair centers. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16145.map.gz | 557.6 MB | EMDB map data format | |
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Header (meta data) | emd-16145-v30.xml emd-16145.xml | 31 KB 31 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16145_fsc.xml | 19.8 KB | Display | FSC data file |
Images | emd_16145.png | 55.7 KB | ||
Others | emd_16145_half_map_1.map.gz emd_16145_half_map_2.map.gz | 557.8 MB 557.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16145 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16145 | HTTPS FTP |
-Validation report
Summary document | emd_16145_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16145_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16145_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | emd_16145_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16145 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16145 | HTTPS FTP |
-Related structure data
Related structure data | 8botMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16145.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:
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-Supplemental data
-Half map: #2
File | emd_16145_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16145_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : NHEJ supercomplex trimer
+Supramolecule #1: NHEJ supercomplex trimer
+Macromolecule #1: DNA repair protein XRCC4
+Macromolecule #2: DNA ligase 4
+Macromolecule #3: Non-homologous end-joining factor 1
+Macromolecule #4: DNA-dependent protein kinase catalytic subunit
+Macromolecule #5: X-ray repair cross-complementing protein 6
+Macromolecule #6: X-ray repair cross-complementing protein 5
+Macromolecule #7: DNA (28-MER)
+Macromolecule #8: DNA (27-MER)
+Macromolecule #9: DNA (24-MER)
+Macromolecule #10: DNA (24-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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 defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / 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 |
+Image processing
-Atomic model buiding 1
Refinement | Overall B value: 639 |
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Output model | PDB-8bot: |