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3.6 Angstrom resolution MAVS filament generated from helical reconstruction

by helical reconstruction, at 3.64 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3.5, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.5, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5922
Title3.6 Angstrom resolution MAVS filament generated from helical reconstruction
Map3.6 Angstrom resolution MAVS filament generated from helical reconstruction
SampleMAVS filament
KeywordsCARD, MAVS, innate immunity, RIG-I, MDA5, spontaneous filament formation
AuthorsWu B, Peisley A, Li Z, Egelman E, Walz T, Penczek P, Hur S
DateDeposition: 2014-03-12, Header release: 2014-07-30, Map release: 2014-07-30, Last update: 2015-07-15
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3.5, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.5, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleMol. Cell, Vol. 55, Issue 4, Page 511-523, Year 2014
TitleMolecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I.
AuthorsBin Wu, Alys Peisley, David Tetrault, Zongli Li, Edward H Egelman, Katharine E Magor, Thomas Walz, Pawel A Penczek, Sun Hur
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115, USA.
Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
Department of Biochemistry and Molecular Biology, The University of Texas-Houston Medical School, Houston, TX 77030, USA.
KeywordsAdaptor Proteins, Signal Transducing (chemistry), Binding Sites (physiology), DEAD-box RNA Helicases (chemistry, 3.6.4.13), Microscopy, Electron, Models, Molecular, Molecular Imprinting (methods), Protein Conformation, Protein Structure, Quaternary, Protein Structure, Tertiary, RNA, Viral (genetics)
LinksPubMed: 25018021, PII: S1097-2765(14)00492-4, DOI: 10.1016/j.molcel.2014.06.010, PMC: PMC4142144
Map
Fileemd_5922.map.gz ( map file in CCP4 format, 12801 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
0.62 A/pix
= 79.36 A
160 pix
0.62 A/pix
= 99.2 A
160 pix
0.62 A/pix
= 99.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:3 (by emdb), 3.5 (movie #1):
Minimum - Maximum: -1.05258262 - 9.2216835
Average (Standard dev.): 0.88586605 (1.48749304)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160128
Origin-80-80-64
Limit797963
Spacing160160128
Unit CellA: 99.2 A, B: 99.2 A, C: 79.36 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 0.62 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-80-80-64
NC/NR/NS160160128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.0539.2220.886
Annotation Details3.6 Angstrom resolution MAVS filament generated from helical reconstruction
Supplement
Sample
NameMAVS filament
Number of Components1
Oligomeric Statefilament
Theoretical Mass0.15MDa
DetailsThe density is only a section of the filament.
Mass-estimation MethodSize exclusion chromatography
Experimental Mass0.15MDa
Component #1: protein - MAVS
Scientific nameMitochondria Anti-viral Signaling protein, CARD domain
Common NameMAVS
Oligomeric Detailsfilament
Scientific Name of SpeciesHomo sapiens
Common Name of Specieshuman
NCBI taxonomy9606
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Exp System Strain: BL21(DE3)
LinksUni Prot: Q7Z434
Experiment
Sample Preparation
Helical ParametersDelta Z: 5.13 A
Delta Phi: 101.1 degrees
Axial Symmetry: C1
Hand: LEFT HANDED
Specimen Statefilament
Specimen Conc0.2 mg/ml
Specimen Support Detailsglow-discharged Quantifoil R1.2/1.3 holey carbon grids
BufferpH: 7.5
Details: 20 mM Tris, 150 mM NaCl
Vitrification
Cryogen NameNITROGEN
InstrumentFEI VITROBOT MARK I
Imaging
MicroscopeFEI TECNAI F20
Date10-AUG-2013
DetailsMovies 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 SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose31 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 29000, Calibrated: 40410
Imaging ModeBRIGHT FIELD
Energy FilterEnergy Filter: FEI
Specimen Holder
ModelGATAN LIQUID NITROGEN
Camera
DetectorGATAN K2 (4k x 4k)
Image Acquisition
#1
Number of Digital Images1863
Processing
Methodhelical reconstruction
3D reconstruction
SoftwareHelicon
Resolution By Author3.64 A
Resolution MethodFSC 0.5, semi-independent
Helical
DetailsThe electron density map of the filament was reconstructed using a helical geometrically constrained reconstruction approach (Helicon).
Download
Data from EMDB
Header (meta data in XML format)emd-5922.xml (7.2 KB)
Map dataemd_5922.map.gz (8.1 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5922
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 3.4 MB
Session file for UCSF-Chimera, 27.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 3.2 MB
Session file for UCSF-Chimera, 27.1 KB