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- EMDB-5925: 3.6 Angstrom resolution MAVS filament generated from helical reco... -

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Basic information

Entry
Database: EMDB / ID: EMD-5925
Title3.6 Angstrom resolution MAVS filament generated from helical reconstruction, truncated map
Map data3.6 Angstrom resolution MAVS filament generated from helical reconstruction. This map is a truncated portion of EMD-5922.
Sample
  • Sample: MAVS filament
  • Protein or peptide: Mitochondria Anti-viral Signaling protein, CARD domain
KeywordsCARD / MAVS / innate immunity / RIG-I / MDA5 / spontaneous filament formation
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane ...positive regulation of IP-10 production / regulation of peroxisome organization / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / positive regulation of NLRP3 inflammasome complex assembly / 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 / protein serine/threonine kinase binding / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / molecular condensate scaffold activity / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / Evasion by RSV of host interferon responses / mitochondrial membrane / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / protein-macromolecule adaptor activity / defense response to virus / DNA-binding transcription factor binding / molecular adaptor activity / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / 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: 3.64 Å
AuthorsWu B / Peisley A / Li Z / Egelman E / Walz T / Penczek P / Hur S
CitationJournal: Mol Cell / Year: 2014
Title: Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I.
Authors: Bin Wu / Alys Peisley / David Tetrault / Zongli Li / Edward H Egelman / Katharine E Magor / Thomas Walz / Pawel A Penczek / Sun Hur /
Abstract: RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires ...RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires its interaction with the tandem CARDs of RIG-I (2CARD(RIG-I)). However, the precise nature of the interaction between 2CARD(RIG-I) and CARD(MAVS), and how this interaction leads to CARD(MAVS) filament assembly, has been unclear. Here we report a 3.6 Å electron microscopy structure of the CARD(MAVS) filament and a 3.4 Å crystal structure of the 2CARD(RIG-I):CARD(MAVS) complex, representing 2CARD(RIG-I) "caught in the act" of nucleating the CARD(MAVS) filament. These structures, together with functional analyses, show that 2CARD(RIG-I) acts as a template for the CARD(MAVS) filament assembly, by forming a helical tetrameric structure and recruiting CARD(MAVS) along its helical trajectory. Our work thus reveals that signal activation by RIG-I occurs by imprinting its helical assembly architecture on MAVS, a previously uncharacterized mechanism of signal transmission.
History
DepositionMar 14, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 30, 2014-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j6j
  • Surface level: 0.35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5925.gif

Downloads & links

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Map

FileDownload / File: emd_5925.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.6 Angstrom resolution MAVS filament generated from helical reconstruction. This map is a truncated portion of EMD-5922.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.1 Å/pix.
x 96 pix.
= 105.6 Å		1.1 Å/pix.
x 96 pix.
= 105.6 Å		1.1 Å/pix.
x 80 pix.
= 88. 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: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.3 / Movie #1: 0.35
Minimum - Maximum-0.208876 - 1.17795968
Average (Standard dev.)0.03205111 (±0.12706143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions968096
Spacing969680
CellA: 105.600006 Å / B: 105.600006 Å / C: 88.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z969680
origin x/y/z0.0000.0000.000
length x/y/z105.600105.60088.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS809696
D min/max/mean-0.2091.1780.032

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Supplemental data

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Sample components

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Entire : MAVS filament

EntireName: MAVS filament
Components
  • Sample: MAVS filament
  • Protein or peptide: Mitochondria Anti-viral Signaling protein, CARD domain

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Supramolecule #1000: MAVS filament

SupramoleculeName: MAVS filament / type: sample / ID: 1000 / Details: The density is only a section of the filament. / Oligomeric state: filament / Number unique components: 1
Molecular weightExperimental: 150 KDa / Theoretical: 150 KDa / Method: Size exclusion chromatography

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Macromolecule #1: Mitochondria Anti-viral Signaling protein, CARD domain

MacromoleculeName: Mitochondria Anti-viral Signaling protein, CARD domain
type: protein_or_peptide / ID: 1 / Name.synonym: MAVS / Oligomeric state: filament / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)
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

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris, 150 mM NaCl
GridDetails: glow-discharged Quantifoil R1.2/1.3 holey carbon grids
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI F20
Specialist opticsEnergy filter - Name: FEI
DetailsMovies were recorded at liquid nitrogen temperature with a K2 Summit direct detector device camera operated in super-resolution mode with dose-fractionation.
DateAug 10, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 1863 / Average electron dose: 31 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40410 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe electron density map of the filament was reconstructed using a helical geometrically constrained reconstruction approach (Helicon).
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.13 Å
Applied symmetry - Helical parameters - Δ&Phi: 101.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: OTHER / Software - Name: Helicon

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Atomic model buiding 1

Initial modelPDB ID:

3j6j


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: G / Chain - #6 - Chain ID: I / Chain - #7 - Chain ID: L
SoftwareName: Phenix
Detailsphenix.refine
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 136 / Target criteria: R-factor
Output model

PDB-3j6j:
3.6 Angstrom resolution MAVS filament generated from helical reconstruction

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