+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5444 | |||||||||
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Title | MDA5-dsRNA filament | |||||||||
Map data | reconstruction of MDA5-dsRNA | |||||||||
Sample |
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Keywords | MAVS nucleation / nucleoprotein filament / helical polymer | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | helical reconstruction / Resolution: 20.0 Å | |||||||||
Authors | Berke IC / Yu X / Modis Y / Egelman EH | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: MDA5 assembles into a polar helical filament on dsRNA. Authors: Ian C Berke / Xiong Yu / Yorgo Modis / Edward H Egelman / Abstract: Melanoma differentiation-associated protein 5 (MDA5) detects viral dsRNA in the cytoplasm. On binding of RNA, MDA5 forms polymers, which trigger assembly of the signaling adaptor mitochondrial ...Melanoma differentiation-associated protein 5 (MDA5) detects viral dsRNA in the cytoplasm. On binding of RNA, MDA5 forms polymers, which trigger assembly of the signaling adaptor mitochondrial antiviral-signaling protein (MAVS) into its active fibril form. The molecular mechanism of MDA5 signaling is not well understood, however. Here we show that MDA5 forms helical filaments on dsRNA and report the 3D structure of the filaments using electron microscopy (EM) and image reconstruction. MDA5 assembles into a polar, single-start helix around the RNA. Fitting of an MDA5 homology model into the structure suggests a key role for the MDA5 C-terminal domain in cooperative filament assembly. Our study supports a signal transduction mechanism in which the helical array of MDA5 within filaments nucleates the assembly of MAVS fibrils. We conclude that MDA5 is a polymerization-dependent signaling platform that uses the amyloid-like self-propagating properties of MAVS to amplify signaling. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5444.map.gz | 314.1 KB | EMDB map data format | |
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Header (meta data) | emd-5444-v30.xml emd-5444.xml | 7.4 KB 7.4 KB | Display Display | EMDB header |
Images | emd_5444_1.png | 89.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5444 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5444 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5444.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of MDA5-dsRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : MDA5-dsRNA
Entire | Name: MDA5-dsRNA |
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Components |
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-Supramolecule #1000: MDA5-dsRNA
Supramolecule | Name: MDA5-dsRNA / type: sample / ID: 1000 / Number unique components: 2 |
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-Macromolecule #1: MDA5
Macromolecule | Name: MDA5 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: Mouse |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Processing | helical reconstruction |
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Aggregation state | filament |
-Sample preparation
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | May 1, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 4.16 µm / Bits/pixel: 14 |
Electron beam | Acceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER |
-Image processing
Details | The particles were processed using IHRSR |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 43.6 Å Applied symmetry - Helical parameters - Δ&Phi: 82.7 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider |