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- EMDB-5444: MDA5-dsRNA filament -

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Basic information

Entry
Database: EMDB / ID: EMD-5444
TitleMDA5-dsRNA filament
Map datareconstruction of MDA5-dsRNA
Sample
  • Sample: MDA5-dsRNA
  • Protein or peptide: MDA5
KeywordsMAVS nucleation / nucleoprotein filament / helical polymer
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / Resolution: 20.0 Å
AuthorsBerke IC / Yu X / Modis Y / Egelman EH
CitationJournal: 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
DepositionJul 4, 2012-
Header (metadata) releaseAug 1, 2012-
Map releaseOct 24, 2012-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5444_1.png

Downloads & links

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Map

FileDownload / File: emd_5444.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of MDA5-dsRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.16 Å/pix.
x 100 pix.
= 416. Å		4.16 Å/pix.
x 100 pix.
= 416. Å		4.16 Å/pix.
x 100 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.175 / Movie #1: 0.2
Minimum - Maximum-0.55990613 - 0.99548107
Average (Standard dev.)0.00007994 (±0.08073194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.164.164.16
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.5600.9950.000

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Supplemental data

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Sample components

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Entire : MDA5-dsRNA

EntireName: MDA5-dsRNA
Components
  • Sample: MDA5-dsRNA
  • Protein or peptide: MDA5

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Supramolecule #1000: MDA5-dsRNA

SupramoleculeName: MDA5-dsRNA / type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: MDA5

MacromoleculeName: MDA5 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
DateMay 1, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 4.16 µm / Bits/pixel: 14
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: OTHER

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Image processing

DetailsThe particles were processed using IHRSR
Final reconstructionApplied 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

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