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Open data
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Basic information
Entry | Database: PDB / ID: 6zh2 | ||||||
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Title | Cryo-EM structure of DNA-PKcs (State 1) | ||||||
![]() | DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-PKcs | ||||||
![]() | DNA BINDING PROTEIN / Kinase / DNA-PKcs / NHEJ / DNA-repair / DNA-PK | ||||||
Function / homology | ![]() 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 / ectopic germ cell programmed cell death / somitogenesis / mitotic G1 DNA damage checkpoint signaling / activation of innate immune response / telomere maintenance / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / small-subunit processome / positive regulation of translation / protein-DNA complex / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / peptidyl-threonine phosphorylation / protein destabilization / protein modification process / brain development / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / rhythmic process / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell differentiation in thymus / double-stranded DNA binding / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / nucleolus / negative regulation of apoptotic process / 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 | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å | ||||||
![]() | Chaplin, A.K. / Hardwick, S.W. / Chirgadze, D.Y. / Blundell, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 655.6 KB | Display | ![]() |
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PDB format | ![]() | 527.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11211MC ![]() 6zfpC ![]() 6zh4C ![]() 6zh6C ![]() 6zh8C ![]() 6zhaC ![]() 6zheC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 472056.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered ...Details: UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily,UNK residues (X) are unknown elements of the DNA-PKcs molecule that have been numbered arbitrarily Source: (natural) ![]() References: UniProt: P78527, non-specific serine/threonine protein kinase |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: DNA-PKcs (state 1) / 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: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 53.95 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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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: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38575 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 142.6 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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