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

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Entry
Database: EMDB / ID: 5890
TitleCryo-EM structure of MAVS CARD filament
Map dataCryo-EM map of MAVS CARD filament
SampleMAVS CARD filament
  • Mitochondrial antiviral-signaling protein (MAVS)
KeywordsInnate immunity / helical filament
Function / homologyOvarian tumor domain proteases / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / TRAF3-dependent IRF activation pathway / Mitochondrial antiviral-signalling protein / Caspase recruitment domain / TRAF6 mediated NF-kB activation / TRAF6 mediated IRF7 activation / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Caspase recruitment domain ...Ovarian tumor domain proteases / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / TRAF3-dependent IRF activation pathway / Mitochondrial antiviral-signalling protein / Caspase recruitment domain / TRAF6 mediated NF-kB activation / TRAF6 mediated IRF7 activation / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Caspase recruitment domain / positive regulation of IP-10 production / regulation of peroxisome organization / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of response to cytokine stimulus / positive regulation of interferon-beta secretion / CARD domain binding / positive regulation of tumor necrosis factor secretion / positive regulation of type I interferon-mediated signaling pathway / positive regulation of interferon-alpha secretion / cellular response to exogenous dsRNA / peroxisomal membrane / positive regulation of interferon-alpha production / positive regulation of interferon-beta production / activation of innate immune response / positive regulation of defense response to virus by host / positive regulation of interleukin-6 secretion / go:0042993: / mitochondrial membrane / positive regulation of interleukin-8 production / negative regulation of viral genome replication / positive regulation of protein import into nucleus, translocation / positive regulation of tumor necrosis factor production / negative regulation of type I interferon production / defense response to virus / go:0004871: / positive regulation of DNA binding transcription factor activity / mitochondrial outer membrane / positive regulation of I-kappaB kinase/NF-kappaB signaling / protein deubiquitination / positive regulation of protein phosphorylation / defense response to bacterium / viral process / protein kinase binding / innate immune response / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / integral component of membrane / Mitochondrial antiviral-signaling protein
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 9.6 Å resolution
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.
Validation ReportPDB-ID: 3j6c

SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2014 / Header (metadata) release: Feb 19, 2014 / Map release: Mar 5, 2014 / Last update: Oct 7, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.52
  • Imaged by UCSF Chimera
  • Download
  • 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 models: PDB-3j6c
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5890.map.gz (map file in CCP4 format, 978 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.333 Å
Density
Contour Level:0.52 (by author), 0.52 (movie #1):
Minimum - Maximum-4.69236183 - 6.60222197
Average (Standard dev.)0.36144659 (0.89477062)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions5050100
Origin000
Limit494999
Spacing5050100
CellA: 116.649994 Å / B: 116.649994 Å / C: 233.29999 Å
α=β=γ: 90 deg.

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 / Number of components: 1 / Oligomeric State: polymer
MassTheoretical: 546 kDa

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Component #1: protein, Mitochondrial antiviral-signaling protein (MAVS)

ProteinName: Mitochondrial antiviral-signaling protein (MAVS) / a.k.a: IPS1, KIAA1271, VISA / Oligomeric Details: polymer / Recombinant expression: Yes
MassTheoretical: 13 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pcDNA3 / Cell of expression system: HEK293T
External referencesUniProt: UniProt:Q7Z434

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C3 (3 fold cyclic) / Hand: LEFT HANDED / Delta z: 16.8 Å / Delta phi: 53.6 deg.
Sample solutionBuffer solution: 20mM Tris-HCl, 50mM NaCl, 1mM DTT / pH: 7.5
Support filmQuantifoil grids coated with thin carbon on top
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Oct 20, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal), 61950 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 100,000x magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2000 nm / Energy filter: JEOL omega filter / Energy window: 0-35 eV
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 7 microns / URL of raw data: http://dx.doi.org/10.6019/EMPIAR-10014
Raw dataEMPIAR-10014 (Title: MAVS CARD and DeltaProTM filaments / Data size: 35.3 GB / Data #1: CARD set1 micrographs [micrographs - single frame] / Data #2: CARD set2 micrographs [micrographs - single frame] / Data #3: CARD set3 micrographs [micrographs - single frame] / Data #4: CARD set4 micrographs [micrographs - single frame]
Data #5: CARD set1 segments [picked particles - single frame - unprocessed]
Data #6: CARD set2 segments [picked particles - single frame - unprocessed]
Data #7: CARD set3 segments [picked particles - single frame - unprocessed]
Data #8: CARD set4 segments [picked particles - single frame - unprocessed]
Data #9: DeltProTM micrographs [micrographs - single frame]
Data #10: DeltaProTM segments [picked particles - single frame - unprocessed])

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Image processing

ProcessingMethod: helical reconstruction / Details: IHRSR
3D reconstructionAlgorithm: IHRSR / Software: Spider, MRC, EMAN, IMAGIC4D / CTF correction: Each filament segment
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.
Resolution: 9.6 Å / Resolution method: FSC 0.5, gold-standard

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Atomic model buiding

Modeling #1Software: Chimera, SITUS / Refinement protocol: rigid body / Refinement space: REAL
Details: The 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.
Input PDB model: 2VGQ
Chain ID: A
Output model

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