+Open data
-Basic information
Entry | Database: PDB / ID: 8ag4 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Vaccinia C16 protein bound to Ku70/Ku80 | |||||||||||||||||||||
Components |
| |||||||||||||||||||||
Keywords | VIRAL PROTEIN / C16 vaccinia virus protein Ku70/Ku80 DNA binding inhibition | |||||||||||||||||||||
Function / homology | Function and homology information Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / protein localization to chromosome, telomeric region / cellular response to fatty acid / positive regulation of neurogenesis / cellular hyperosmotic salinity response / hematopoietic stem cell proliferation / positive regulation of catalytic activity / telomeric DNA binding / 2-LTR circle formation / : / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / cyclin binding / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / neurogenesis / enzyme activator activity / positive regulation of telomere maintenance via telomerase / activation of innate immune response / DNA helicase activity / telomere maintenance / cellular response to leukemia inhibitory factor / Nonhomologous End-Joining (NHEJ) / small-subunit processome / protein-DNA complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-strand break repair / double-stranded DNA binding / chromosome, telomeric region / scaffold protein binding / transcription regulator complex / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription cis-regulatory region binding / damaged DNA binding / ribonucleoprotein complex / response to xenobiotic stimulus / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) Vaccinia virus Western Reserve | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å | |||||||||||||||||||||
Authors | Rivera-Calzada, A. / Arribas-Bosacoma, R. / Pearl, L.H. / Llorca, O. | |||||||||||||||||||||
Funding support | Spain, United Kingdom, 6items
| |||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus. Authors: Angel Rivera-Calzada / Raquel Arribas-Bosacoma / Alba Ruiz-Ramos / Paloma Escudero-Bravo / Jasminka Boskovic / Rafael Fernandez-Leiro / Antony W Oliver / Laurence H Pearl / Oscar Llorca / Abstract: Detection of cytosolic DNA is a central element of the innate immunity system against viral infection. The Ku heterodimer, a component of the NHEJ pathway of DNA repair in the nucleus, functions as ...Detection of cytosolic DNA is a central element of the innate immunity system against viral infection. The Ku heterodimer, a component of the NHEJ pathway of DNA repair in the nucleus, functions as DNA sensor that detects dsDNA of viruses that replicate in the cytoplasm. Vaccinia virus expresses two proteins, C4 and C16, that inactivate DNA sensing and enhance virulence. The structural basis for this is unknown. Here we determine the structure of the C16 - Ku complex using cryoEM. Ku binds dsDNA by a preformed ring but C16 sterically blocks this access route, abrogating binding to a dsDNA end and its insertion into DNA-PK, thereby averting signalling into the downstream innate immunity system. C4 replicates these activities using a domain with 54% identity to C16. Our results reveal how vaccinia virus subverts the capacity of Ku to recognize viral DNA. | |||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ag4.cif.gz | 301.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ag4.ent.gz | 230.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ag4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8ag4 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8ag4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 15415MC 8ag3C 8ag5C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 74234.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Plasmid: pFASTBAC-HTb / Production host: Trichoplusia ni (cabbage looper) 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 |
---|---|
#2: Protein | Mass: 85546.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Plasmid: pFASTBAC-HTb / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
#3: Protein | Mass: 42476.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus Western Reserve / Strain: Western Reserve / Gene: VACWR010, C10L, VACWR209 / Plasmid: pET-52b(+) Details (production host): Original plasmid modified so MCS contains TEV-TwinStrep Production host: Escherichia coli (E. coli) / References: UniProt: P03296 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Vaccinia C16 protein bound to Ku70/Ku80 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.230 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 13216 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 12495814 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 579038 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Initial model for chains C and D was generated using AlphaFold2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 1JEY / Initial refinement model-ID: 1 / PDB-ID: 1JEY / Source name: PDB / Type: experimental model
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|