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- PDB-7nic: CryoEM structure of disease related M854K MDA5-dsRNA filament in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nic | |||||||||
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Title | CryoEM structure of disease related M854K MDA5-dsRNA filament in complex with ADP-AlF4(minor class) | |||||||||
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![]() | ANTIVIRAL PROTEIN / PROTEIN-RNA COMPLEX / HELICAL FILAMENT / ATPASE / INNATE IMMUNE RECEPTOR / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() MDA-5 signaling pathway / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / 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 / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / positive regulation of interferon-alpha production / protein sumoylation / ribonucleoprotein complex binding / antiviral innate immune response / positive regulation of interferon-beta production / response to virus / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / protein complex oligomerization / 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 | ![]() ![]() synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Yu, Q. / Modis, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.7 KB | Display | ![]() |
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PDB format | ![]() | 212.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12294MC ![]() 7bkpC ![]() 7bkqC ![]() 7ngaC ![]() 7niqC C: citing same article ( M: map data used to model this data |
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Similar structure data | |
EM raw data | ![]() Data size: 2.5 TB Data #1: Unaligned multi-frame micrographs of MDA5 variant M854K bound to dsRNA and ADP-ALF4 [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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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 Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-RNA chain , 2 types, 2 molecules XY
#2: RNA chain | Mass: 4894.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Pseudomonas virus phi6 Tax ID 10879 / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 4681.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Pseudomonas virus phi6 Tax ID 10879 / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ALF.gif)
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#4: Chemical | ChemComp-ADP / |
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#5: Chemical | ChemComp-ALF / |
#6: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.7 | ||||||||||||||||||||||||||||||
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: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.2 K Details: Grids were blotted for 3 s; blot force 10, 5, 0, -5, -10 |
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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 / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 29.6 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
EM imaging optics | Phase plate: OTHER / Spherical aberration corrector: none |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 88.0297 ° / Axial rise/subunit: 45.0795 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 731263 | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62028 / Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||
Atomic model building | B value: 147 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6GKH Accession code: 6GKH / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 125.79 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints |
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