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- EMDB-5890: Cryo-EM structure of MAVS CARD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-5890
TitleCryo-EM structure of MAVS CARD filament
Map dataCryo-EM map of MAVS CARD filament
Sample
  • Sample: MAVS CARD filament
  • Protein or peptide: Mitochondrial antiviral-signaling protein (MAVS)
KeywordsInnate immunity / helical filament
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / CARD domain binding / positive regulation of myeloid dendritic cell cytokine production / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / CARD domain binding / positive regulation of myeloid dendritic cell cytokine production / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / peroxisomal membrane / cellular response to exogenous dsRNA / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of NLRP3 inflammasome complex assembly / type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / positive regulation of type I interferon production / positive regulation of defense response to virus by host / signaling adaptor activity / ubiquitin ligase complex / activation of innate immune response / antiviral innate immune response / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / molecular condensate scaffold activity / positive regulation of DNA-binding transcription factor activity / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / Evasion by RSV of host interferon responses / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / molecular adaptor activity / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding
Similarity search - Function
IPS1, CARD domain / : / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsXu H / He X / Zheng H / Huang LJ / Hou F / Yu Z / de la Cruz MJ / Borkowski B / Zhang X / Chen ZJ / Jiang Q-X
CitationJournal: Elife / Year: 2014
Title: Structural basis for the prion-like MAVS filaments in antiviral innate immunity.
Authors: Hui Xu / Xiaojing He / Hui Zheng / Lily J Huang / Fajian Hou / Zhiheng Yu / Michael Jason de la Cruz / Brian Borkowski / Xuewu Zhang / Zhijian J Chen / Qiu-Xing Jiang /
Abstract: Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling ...Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments. DOI: http://dx.doi.org/10.7554/eLife.01489.001.
History
DepositionJan 22, 2014-
Header (metadata) releaseFeb 19, 2014-
Map releaseMar 5, 2014-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.52
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.52
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j6c
  • Surface level: 0.52
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6c
  • Surface level: 0.52
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6c
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5890.tif

Downloads & links

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Map

FileDownload / File: emd_5890.map.gz / Format: CCP4 / Size: 955.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of MAVS CARD filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.33 Å/pix.
x 100 pix.
= 233.3 Å		2.33 Å/pix.
x 50 pix.
= 116.65 Å		2.33 Å/pix.
x 50 pix.
= 116.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.52 / Movie #1: 0.52
Minimum - Maximum-4.69236183 - 6.60222197
Average (Standard dev.)0.36144659 (±0.89477062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions5050100
Spacing5050100
CellA: 116.649994 Å / B: 116.649994 Å / C: 233.29999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.3332.3332.333
M x/y/z5050100
origin x/y/z0.0000.0000.000
length x/y/z116.650116.650233.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS5050100
D min/max/mean-4.6926.6020.361

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Supplemental data

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Sample components

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Entire : MAVS CARD filament

EntireName: MAVS CARD filament
Components
  • Sample: MAVS CARD filament
  • Protein or peptide: Mitochondrial antiviral-signaling protein (MAVS)

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Supramolecule #1000: MAVS CARD filament

SupramoleculeName: MAVS CARD filament / type: sample / ID: 1000 / Oligomeric state: polymer / Number unique components: 1
Molecular weightTheoretical: 546 KDa

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Macromolecule #1: Mitochondrial antiviral-signaling protein (MAVS)

MacromoleculeName: Mitochondrial antiviral-signaling protein (MAVS) / type: protein_or_peptide / ID: 1 / Name.synonym: IPS1, KIAA1271, VISA / Oligomeric state: polymer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 13 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T / Recombinant plasmid: pcDNA3
SequenceUniProtKB: Mitochondrial antiviral-signaling protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5 / Details: 20mM Tris-HCl, 50mM NaCl, 1mM DTT
GridDetails: Quantifoil grids coated with thin carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL 2200FS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000x magnification
Specialist opticsEnergy filter - Name: JEOL omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 35.0 eV
DateOct 20, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 61950 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsIHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 16.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 53.6 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: OTHER / Software - Name: Spider, MRC, EMAN, IMAGIC4D
Details: Final data were calculated from three separate datasets from three sessions of data collection. The handedness of the map was determined by cryo-electron tomography.
CTF correctionDetails: Each filament segment

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Atomic model buiding 1

Initial modelPDB ID:

2vgq


Chain - Chain ID: A
SoftwareName: Chimera, SITUS
DetailsThe docking of one X-ray model into a segmented map corresponding to one subunit was first done manually in Chimera, and then optimized using SITUS.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j6c:
Cryo-EM structure of MAVS CARD filament

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