|Entry||Database: EMDB / ID: 5922|
|Title||3.6 Angstrom resolution MAVS filament generated from helical reconstruction|
|Map data||3.6 Angstrom resolution MAVS filament generated from helical reconstruction|
|Keywords||CARD / MAVS / innate immunity / RIG-I / MDA5 / spontaneous filament formation|
|Function / homology||TRAF6 mediated IRF7 activation / Mitochondrial antiviral-signalling protein / TRAF3-dependent IRF activation pathway / Negative regulators of DDX58/IFIH1 signaling / Ovarian tumor domain proteases / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Caspase recruitment domain / Caspase recruitment domain / TRAF6 mediated NF-kB activation ...TRAF6 mediated IRF7 activation / Mitochondrial antiviral-signalling protein / TRAF3-dependent IRF activation pathway / Negative regulators of DDX58/IFIH1 signaling / Ovarian tumor domain proteases / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Caspase recruitment domain / Caspase recruitment domain / TRAF6 mediated NF-kB activation / 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 / cellular response to exogenous dsRNA / peroxisomal membrane / positive regulation of interferon-alpha production / positive regulation of interferon-alpha secretion / 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 / negative regulation of type I interferon production / 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 / 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 / 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
|Source||Homo sapiens (human)|
|Method||helical reconstruction / cryo EM / 3.64 Å resolution|
|Authors||Wu B / Peisley A / Li Z / Egelman E / Walz T / Penczek P / Hur S|
|Citation||Journal: 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.
|Date||Deposition: Mar 12, 2014 / Header (metadata) release: Jul 30, 2014 / Map release: Jul 30, 2014 / Last update: Jul 15, 2015|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5922.map.gz (map file in CCP4 format, 12801 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.62 Å|
CCP4 map header:
-Entire MAVS filament
|Entire||Name: MAVS filament / Details: The density is only a section of the filament. / Number of components: 1 / Oligomeric State: filament|
|Mass||Theoretical: 150 kDa / Experimental: 150 kDa / Measured by: Size exclusion chromatography|
-Component #1: protein, Mitochondria Anti-viral Signaling protein, CARD domain
|Protein||Name: Mitochondria Anti-viral Signaling protein, CARD domain|
a.k.a: MAVSDallas Mavericks / Oligomeric Details: filament / Recombinant expression: Yes
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Strain: BL21(DE3)|
|External references||UniProt: Mitochondrial antiviral-signaling protein|
|Specimen||Specimen state: filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Hand: LEFT HANDED / Delta z: 5.13 Å / Delta phi: 101.1 deg.|
|Sample solution||Specimen conc.: 0.2 mg/ml / Buffer solution: 20 mM Tris, 150 mM NaCl / pH: 7.5|
|Support film||glow-discharged Quantifoil R1.2/1.3 holey carbon grids|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: NITROGEN|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Aug 10, 2013|
Details: Movies were recorded at liquid nitrogen temperature with a K2 Summit direct detector device camera operated in super-resolution mode with dose-fractionation.
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 31 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 29000 X (nominal), 40410 X (calibrated) / Imaging mode: BRIGHT FIELD / Energy filter: FEI|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 1863|
|Processing||Method: helical reconstruction|
Details: The electron density map of the filament was reconstructed using a helical geometrically constrained reconstruction approach (Helicon).
|3D reconstruction||Software: Helicon / Resolution: 3.64 Å / Resolution method: FSC 0.5, semi-independent|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi