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Yorodumi- PDB-7bkp: CryoEM structure of disease related M854K MDA5-dsRNA filament in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bkp | |||||||||
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Title | CryoEM structure of disease related M854K MDA5-dsRNA filament in complex with ATP | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / PROTEIN-RNA COMPLEX / HELICAL FILAMENT / ATPASE / INNATE IMMUNE RECEPTOR | |||||||||
Function / homology | Function and homology information MDA-5 signaling pathway / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / cellular response to exogenous dsRNA / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / protein sumoylation / ribonucleoprotein complex binding ...MDA-5 signaling pathway / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / cellular response to exogenous dsRNA / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / protein sumoylation / ribonucleoprotein complex binding / antiviral innate immune response / positive regulation of interferon-beta production / protein complex oligomerization / response to virus / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / RNA helicase / protein domain specific binding / innate immune response / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Pseudomonas virus phi6 (bacteriophage) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Singh, R. / Herrero del Valle, A. / Yu, Q. / Modis, Y. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA. Authors: Qin Yu / Alba Herrero Del Valle / Rahul Singh / Yorgo Modis / Abstract: Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. ...Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoinflammatory disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more stably to synthetic Alu:Alu dsRNA. CryoEM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 sidechain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle- RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via an allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides insights on how MDA5 recognizes dsRNA in health and disease. | |||||||||
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 | 7bkp.cif.gz | 277.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bkp.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bkp_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7bkp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7bkp_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 7bkp_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/7bkp ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bkp | HTTPS FTP |
-Related structure data
Related structure data | 12213MC 7bkqC 7ngaC 7nicC 7niqC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10630 (Title: CryoEM structure of disease related M854K MDA5-dsRNA filament in complex with ATP Data size: 1.2 TB Data #1: Unaligned multi frame micrographs for the Cryo-EM structure of disease related M854K MDA5-dsRNA filament in complex with ATP [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 116122.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ATP / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifih1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8R5F7, RNA helicase |
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-RNA chain , 2 types, 2 molecules ZX
#2: RNA chain | Mass: 4352.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas virus phi6 (bacteriophage) |
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#3: RNA chain | Mass: 4587.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas virus phi6 (bacteriophage) |
-Non-polymers , 3 types, 3 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-ATP / |
#6: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: machine step 6 / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.2 K Details: Grids were blotted for 3 s; blot force 10, 5, 0, -5, -10 |
-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: DARK FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -1200 nm / Calibrated defocus min: -250 nm / Calibrated defocus max: -4000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7147 |
EM imaging optics | Energyfilter slit width: 20 eV / Phase plate: OTHER / Spherical aberration corrector: none |
Image scans | Width: 5760 / Height: 4092 |
-Processing
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EM software |
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Image processing | Details: The images were motion-corrected | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 74.63 ° / Axial rise/subunit: 43.92 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1068108 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 383128 / Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 50 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6G19 Accession code: 6G19 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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