[English] 日本語
Yorodumi
- EMDB-5922: 3.6 Angstrom resolution MAVS filament generated from helical reco... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5922
Title3.6 Angstrom resolution MAVS filament generated from helical reconstruction
Map data3.6 Angstrom resolution MAVS filament generated from helical reconstruction
SampleMAVS filament
  • Mitochondria Anti-viral Signaling protein, CARD domain
KeywordsCARD / MAVS / innate immunity / RIG-I / MDA5 / spontaneous filament formation
Function / homologyTRAF6 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
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.64 Å resolution
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.
DateDeposition: Mar 12, 2014 / Header (metadata) release: Jul 30, 2014 / Map release: Jul 30, 2014 / Last update: Jul 15, 2015

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_5922.map.gz (map file in CCP4 format, 12801 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
0.62 Å/pix.
= 79.36 Å
160 pix
0.62 Å/pix.
= 99.2 Å
160 pix
0.62 Å/pix.
= 99.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.62 Å
Density
Contour Level:3 (by emdb), 3.5 (movie #1):
Minimum - Maximum-1.05258262 - 9.2216835
Average (Standard dev.)0.88586605 (1.48749304)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160128
Origin-80-80-64
Limit797963
Spacing160160128
CellA: 99.2 Å / B: 99.2 Å / C: 79.36 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.620.620.62
M x/y/z160160128
origin x/y/z0.0000.0000.000
length x/y/z99.20099.20079.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-80-80-64
NC/NR/NS160160128
D min/max/mean-1.0539.2220.886

-
Supplemental data

-
Sample components

-
Entire MAVS filament

EntireName: MAVS filament / Details: The density is only a section of the filament. / Number of components: 1 / Oligomeric State: filament
MassTheoretical: 150 kDa / Experimental: 150 kDa / Measured by: Size exclusion chromatography

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

ProteinName: Mitochondria Anti-viral Signaling protein, CARD domain
a.k.a: MAVSDallas Mavericks / Oligomeric Details: filament / Recombinant expression: Yes
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: BL21(DE3)
External referencesUniProt: Mitochondrial antiviral-signaling protein

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: LEFT HANDED / Delta z: 5.13 Å / Delta phi: 101.1 deg.
Sample solutionSpecimen conc.: 0.2 mg/ml / Buffer solution: 20 mM Tris, 150 mM NaCl / pH: 7.5
Support filmglow-discharged Quantifoil R1.2/1.3 holey carbon grids
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: NITROGEN

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: 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 gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 31 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal), 40410 X (calibrated) / Imaging mode: BRIGHT FIELD / Energy filter: FEI
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1863

-
Image processing

ProcessingMethod: helical reconstruction
Details: The electron density map of the filament was reconstructed using a helical geometrically constrained reconstruction approach (Helicon).
3D reconstructionSoftware: Helicon / Resolution: 3.64 Å / Resolution method: FSC 0.5, semi-independent

+
About Yorodumi

-
News

-
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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more

-
Yorodumi

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

Read more