[English] 日本語
Yorodumi- EMDB-5925: 3.6 Angstrom resolution MAVS filament generated from helical reco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5925 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 3.6 Angstrom resolution MAVS filament generated from helical reconstruction, truncated map | |||||||||
Map data | 3.6 Angstrom resolution MAVS filament generated from helical reconstruction. This map is a truncated portion of EMD-5922. | |||||||||
Sample |
| |||||||||
Keywords | CARD / 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 / 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 / activation of innate immune response / ubiquitin ligase complex / 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 / mitochondrial membrane / positive regulation of DNA-binding transcription factor activity / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / Evasion by RSV of host interferon responses / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.64 Å | |||||||||
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. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5925.map.gz | 2.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5925-v30.xml emd-5925.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | 400_5925.gif 80_5925.gif | 87.6 KB 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5925 | HTTPS FTP |
-Validation report
Summary document | emd_5925_validation.pdf.gz | 302.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_5925_full_validation.pdf.gz | 302.5 KB | Display | |
Data in XML | emd_5925_validation.xml.gz | 4.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5925 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5925 | HTTPS FTP |
-Related structure data
Related structure data | 3j6jMC 5922C 4p4hC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_5925.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3.6 Angstrom resolution MAVS filament generated from helical reconstruction. This map is a truncated portion of EMD-5922. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : MAVS filament
Entire | Name: MAVS filament |
---|---|
Components |
|
-Supramolecule #1000: MAVS filament
Supramolecule | Name: MAVS filament / type: sample / ID: 1000 / Details: The density is only a section of the filament. / Oligomeric state: filament / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 150 KDa / Theoretical: 150 KDa / Method: Size exclusion chromatography |
-Macromolecule #1: Mitochondria Anti-viral Signaling protein, CARD domain
Macromolecule | Name: 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 expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) |
Sequence | UniProtKB: Mitochondrial antiviral-signaling protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.2 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 20 mM Tris, 150 mM NaCl |
Grid | Details: glow-discharged Quantifoil R1.2/1.3 holey carbon grids |
Vitrification | Cryogen name: NITROGEN / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Specialist optics | Energy filter - Name: FEI |
Details | Movies were recorded at liquid nitrogen temperature with a K2 Summit direct detector device camera operated in super-resolution mode with dose-fractionation. |
Date | Aug 10, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 1863 / Average electron dose: 31 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 40410 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The electron density map of the filament was reconstructed using a helical geometrically constrained reconstruction approach (Helicon). |
---|---|
Final reconstruction | Applied 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 |
-Atomic model buiding 1
Initial model | PDB ID: 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 |
---|---|
Software | Name: Phenix |
Details | phenix.refine |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 136 / Target criteria: R-factor |
Output model | PDB-3j6j: |