+Open data
-Basic information
Entry | Database: PDB / ID: 6zh4 | ||||||
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Title | Cryo-EM structure of DNA-PKcs (State 3) | ||||||
Components | DNA-dependent protein kinase catalytic subunit,DNA-PKcs | ||||||
Keywords | DNA BINDING PROTEIN / Kinase / DNA-PKcs / NHEJ / DNA-repair / DNA-PK | ||||||
Function / homology | Function and homology information positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / 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 ...positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / 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 / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / regulation of epithelial cell proliferation / IRF3-mediated induction of type I IFN / telomere capping / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / T cell lineage commitment / negative regulation of cGAS/STING signaling pathway / double-strand break repair via alternative nonhomologous end joining / maturation of 5.8S rRNA / B cell lineage commitment / positive regulation of double-strand break repair via nonhomologous end joining / mitotic G1 DNA damage checkpoint signaling / ectopic germ cell programmed cell death / somitogenesis / activation of innate immune response / telomere maintenance / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / Nonhomologous End-Joining (NHEJ) / small-subunit processome / positive regulation of translation / regulation of circadian rhythm / protein-DNA complex / response to gamma radiation / peptidyl-threonine phosphorylation / protein destabilization / protein modification process / brain development / cellular response to insulin stimulus / double-strand break repair via nonhomologous end joining / rhythmic process / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / double-stranded DNA binding / heart development / peptidyl-serine phosphorylation / chromosome, telomeric region / T cell differentiation in thymus / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / non-specific serine/threonine protein kinase / protein kinase activity / protein domain specific binding / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / DNA damage response / chromatin / negative regulation of apoptotic process / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å | ||||||
Authors | Chaplin, A.K. / Hardwick, S.W. / Chirgadze, D.Y. / Blundell, T.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Dimers of DNA-PK create a stage for DNA double-strand break repair. Authors: Amanda K Chaplin / Steven W Hardwick / Shikang Liang / Antonia Kefala Stavridi / Ales Hnizda / Lee R Cooper / Taiana Maia De Oliveira / Dimitri Y Chirgadze / Tom L Blundell / Abstract: DNA double-strand breaks are the most dangerous type of DNA damage and, if not repaired correctly, can lead to cancer. In humans, Ku70/80 recognizes DNA broken ends and recruits the DNA-dependent ...DNA double-strand breaks are the most dangerous type of DNA damage and, if not repaired correctly, can lead to cancer. In humans, Ku70/80 recognizes DNA broken ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form DNA-dependent protein kinase holoenzyme (DNA-PK) in the process of non-homologous end joining (NHEJ). We present a 2.8-Å-resolution cryo-EM structure of DNA-PKcs, allowing precise amino acid sequence registration in regions uninterpreted in previous 4.3-Å X-ray maps. We also report a cryo-EM structure of DNA-PK at 3.5-Å resolution and reveal a dimer mediated by the Ku80 C terminus. Central to dimer formation is a domain swap of the conserved C-terminal helix of Ku80. Our results suggest a new mechanism for NHEJ utilizing a DNA-PK dimer to bring broken DNA ends together. Furthermore, drug inhibition of NHEJ in combination with chemo- and radiotherapy has proved successful, making these models central to structure-based drug targeting efforts. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2020 Title: Dimers of DNA-PK create a stage for DNA-double strand break repair Authors: Chaplin, A.K. / Hardwick, S.W. / Liang, S. / Stavridi, A.K. / Hnizda, A. / Cooper, L.R. / De Oliveira, T.M. / Chirgadze, D.Y. / Blundell, T.L. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zh4.cif.gz | 653.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zh4.ent.gz | 527.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zh4_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6zh4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6zh4_validation.xml.gz | 114 KB | Display | |
Data in CIF | 6zh4_validation.cif.gz | 170.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/6zh4 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/6zh4 | HTTPS FTP |
-Related structure data
Related structure data | 11213MC 6zfpC 6zh2C 6zh6C 6zh8C 6zhaC 6zheC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 472056.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA References: UniProt: P78527, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DNA-PKcs / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.47 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 53.95 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
Particle selection | Num. of particles selected: 378084 | |||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47183 / Symmetry type: POINT |