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- EMDB-5891: Cryo-EM structure of MAVSdeltaProTM filament -

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Basic information

Entry
Database: EMDB / ID: EMD-5891
TitleCryo-EM structure of MAVSdeltaProTM filament
Map dataCryo-EM map of filaments formed by a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain
Sample
  • Sample: Filaments formed by a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain
  • Protein or peptide: Mitochondrial antiviral-signaling protein (MAVS)
KeywordsInnate immunity / helical filament / cryoEM / helical reconstruction
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 / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / 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 / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of viral genome replication / positive regulation of NLRP3 inflammasome complex assembly / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / positive regulation of type I interferon production / ubiquitin ligase complex / positive regulation of defense response to virus by host / signaling adaptor activity / antiviral innate immune response / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / positive regulation of DNA-binding transcription factor activity / mitochondrial membrane / molecular condensate scaffold activity / 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 / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / defense response to virus / mitochondrial outer membrane / positive regulation of protein phosphorylation / defense response to bacterium / 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: 16.4 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 23, 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: 0.0339
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0339
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5891.tif

Downloads & links

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Map

FileDownload / File: emd_5891.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of filaments formed by a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.33 Å/pix.
x 80 pix.
= 186.64 Å		2.33 Å/pix.
x 60 pix.
= 139.98 Å		2.33 Å/pix.
x 60 pix.
= 139.98 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: 0.0339 / Movie #1: 0.0339
Minimum - Maximum-0.25457004 - 1.00864923
Average (Standard dev.)0.02374649 (±0.13765344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606080
Spacing606080
CellA: 139.98 Å / B: 139.98 Å / C: 186.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.3332.3332.333
M x/y/z606080
origin x/y/z0.0000.0000.000
length x/y/z139.980139.980186.640
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/NS606080
D min/max/mean-0.2551.0090.024

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Supplemental data

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Sample components

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Entire : Filaments formed by a truncated MAVS lacking part of the proline-...

EntireName: Filaments formed by a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain
Components
  • Sample: Filaments formed by a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain
  • Protein or peptide: Mitochondrial antiviral-signaling protein (MAVS)

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Supramolecule #1000: Filaments formed by a truncated MAVS lacking part of the proline-...

SupramoleculeName: Filaments formed by a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain
type: sample / ID: 1000 / Oligomeric state: polymer / Number unique components: 1
Molecular weightTheoretical: 1.396 MDa

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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: 42.3 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pET28a
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: 8 / Details: 10mM Tris-HCl, 150mM 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 100,000 x magnification
Specialist opticsEnergy filter - Name: JEOL omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 35.0 eV
DateNov 30, 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. Due to the smaller size of the dataset, we did not sort the data based on variations in symmetry parameters.
Final reconstructionApplied symmetry - Helical parameters - Δz: 16.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 52.9 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.4 Å / Resolution method: OTHER / Software - Name: Spider, MRC, EMAN, IMAGIC4D
CTF correctionDetails: Each filament segment

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