+Open data
-Basic information
Entry | Database: PDB / ID: 7sud | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of DNA-PK complex VIII | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / NHEJ / Kinase / DNA repair / DNA-PK | ||||||
Function / homology | Function and homology information 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 ...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 / IRF3-mediated induction of type I IFN / nuclear telomere cap complex / 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 / 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 / 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 / secretory granule lumen / DNA recombination / 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 / 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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Chen, X. / Liu, L. / Gellert, M. / Yang, W. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Mol Cell / Year: 2022 Title: Autophosphorylation transforms DNA-PK from protecting to processing DNA ends. Authors: Lan Liu / Xuemin Chen / Jun Li / Huaibin Wang / Christopher J Buehl / Noah J Goff / Katheryn Meek / Wei Yang / Martin Gellert / Abstract: The DNA-dependent protein kinase (DNA-PK) initially protects broken DNA ends but then promotes their processing during non-homologous end joining (NHEJ). Before ligation by NHEJ, DNA hairpin ends ...The DNA-dependent protein kinase (DNA-PK) initially protects broken DNA ends but then promotes their processing during non-homologous end joining (NHEJ). Before ligation by NHEJ, DNA hairpin ends generated during V(D)J recombination must be opened by the Artemis nuclease, together with autophosphorylated DNA-PK. Structures of DNA-PK bound to DNA before and after phosphorylation, and in complex with Artemis and a DNA hairpin, reveal an essential functional switch. When bound to open DNA ends in its protection mode, DNA-PK is inhibited for cis-autophosphorylation of the so-called ABCDE cluster but activated for phosphorylation of other targets. In contrast, DNA hairpin ends promote cis-autophosphorylation. Phosphorylation of four Thr residues in ABCDE leads to gross structural rearrangement of DNA-PK, widening the DNA binding groove for Artemis recruitment and hairpin cleavage. Meanwhile, Artemis locks DNA-PK into the kinase-inactive state. Kinase activity and autophosphorylation of DNA-PK are regulated by different DNA ends, feeding forward to coordinate NHEJ events. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7sud.cif.gz | 682.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7sud.ent.gz | 552.7 KB | Display | PDB format |
PDBx/mmJSON format | 7sud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sud_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7sud_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7sud_validation.xml.gz | 97.2 KB | Display | |
Data in CIF | 7sud_validation.cif.gz | 149.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/7sud ftp://data.pdbj.org/pub/pdb/validation_reports/su/7sud | HTTPS FTP |
-Related structure data
Related structure data | 25440MC 7sglC 7su3C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 469993.031 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 |
---|---|
#2: 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 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DNA-PK / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
---|---|
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 |
---|---|
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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42521 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|