+Open data
-Basic information
Entry | Database: PDB / ID: 7k1k | ||||||
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Title | CryoEM structure of inactivated-form DNA-PK (Complex IV) | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / NHEJ / V(D)J recombination / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of lymphocyte differentiation / small-subunit processome assembly / Ku70:Ku80 complex / DNA-dependent protein kinase complex / negative regulation of t-circle formation / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / MHC class II antigen presentation / nonhomologous end joining complex / cellular response to X-ray ...positive regulation of lymphocyte differentiation / small-subunit processome assembly / Ku70:Ku80 complex / DNA-dependent protein kinase complex / negative regulation of t-circle formation / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / MHC class II antigen presentation / nonhomologous end joining complex / cellular response to X-ray / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / Neutrophil degranulation / DNA ligation / IRF3-mediated induction of type I IFN / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / entry into host cell by a symbiont-containing vacuole / positive regulation of catalytic activity / U3 snoRNA binding / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / positive regulation of neurogenesis / cellular response to fatty acid / cellular hyperosmotic salinity response / hematopoietic stem cell proliferation / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / telomeric DNA binding / 2-LTR circle formation / : / site of DNA damage / protein autoprocessing / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / activation of innate immune response / enzyme activator activity / transport vesicle / positive regulation of telomere maintenance via telomerase / telomere maintenance / DNA helicase activity / neurogenesis / cyclin binding / protein-DNA complex / cellular response to leukemia inhibitory factor / small-subunit processome / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / protein processing / 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 / aspartic-type endopeptidase activity / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / proteolysis / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Chen, X. / Gellert, M. / Yang, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structure of an activated DNA-PK and its implications for NHEJ. Authors: Xuemin Chen / Xiang Xu / Yun Chen / Joyce C Cheung / Huaibin Wang / Jiansen Jiang / Natalia de Val / Tara Fox / Martin Gellert / Wei Yang / Abstract: DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of ...DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved. For DNA-PK, all existing structures represent inactive states with resolution limited to 4.3 Å at best. Here, we report the cryoelectron microscopy (cryo-EM) structures of DNA-PKcs (DNA-PK catalytic subunit) bound to a DNA end or complexed with Ku70/80 and DNA in both inactive and activated forms at resolutions of 3.7 Å overall and 3.2 Å for FATKINs. These structures reveal the sequential transition of DNA-PK from inactive to activated forms. Most notably, activation of the kinase involves previously unknown stretching and twisting within individual solenoid segments and loosens DNA-end binding. This unprecedented structural plasticity of helical repeats may be a general regulatory mechanism of HEAT-repeat proteins. | ||||||
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 | 7k1k.cif.gz | 867.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k1k.ent.gz | 688.6 KB | Display | PDB format |
PDBx/mmJSON format | 7k1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k1k_validation.pdf.gz | 977.3 KB | Display | wwPDB validaton report |
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Full document | 7k1k_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7k1k_validation.xml.gz | 117.2 KB | Display | |
Data in CIF | 7k1k_validation.cif.gz | 180.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/7k1k ftp://data.pdbj.org/pub/pdb/validation_reports/k1/7k1k | HTTPS FTP |
-Related structure data
Related structure data | 22625MC 7k0yC 7k10C 7k11C 7k17C 7k19C 7k1bC 7k1jC 7k1nC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 469673.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P78527, non-specific serine/threonine protein kinase | ||
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#2: Protein | Mass: 69945.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Production host: Homo sapiens (human) References: UniProt: P12956, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases | ||
#3: Protein | Mass: 82812.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Production host: Homo sapiens (human) References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||
#4: DNA chain | Mass: 7311.714 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: DNA chain | Mass: 4956.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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-PK / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||
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: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96299 / Symmetry type: POINT | ||||||||||||||||||||||||
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