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The structure of the recombinant alphavirus, Western equine encephalitis virus, revealed by cryoelectron microscopy

by single particle (icosahedral) reconstruction, at 12 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 80, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 80, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5210
AuthorsSherman MB, Weaver SC
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 80, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 80, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-1121

EMDB-5388

EMDB-1082

EMDB-1164

EMDB-1301
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Virol., Vol. 84, Issue 19, Page 9775-82, Year 2010
TitleStructure of the recombinant alphavirus Western equine encephalitis virus revealed by cryoelectron microscopy.
AuthorsMichael B Sherman, Scott C Weaver
W. M. Keck Center for Virus Imaging, University of Texas Medical Branch, Galveston, Texas, USA.
KeywordsAlphavirus (ultrastructure), Animals, Containment of Biohazards, Cryoelectron Microscopy, Encephalitis Virus, Venezuelan Equine (ultrastructure), Encephalitis Virus, Western Equine (genetics), Encephalomyelitis, Western Equine (transmission), Genome, Viral, Horse Diseases (transmission), Horses, Humans, Imaging, Three-Dimensional, Models, Molecular, Recombination, Genetic, Sindbis Virus (ultrastructure), Species Specificity, Viral Structural Proteins (chemistry)
LinksDOI: 10.1128/JVI.00876-10, PubMed: 20631130, PMC: PMC2937749
Map
FileEMD-5210.map ( map file in CCP4 format, 188185 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:80 (by author), 80 (movie #1):
Minimum - Maximum: -298.08413696 - 340.75912476
Average (Standard dev.): 9.37805367 (57.56100845)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 361 361 361
Origin : -180 -180 -180
Limit : 180 180 180
Spacing : 361 361 361
Unit CellA = 830.3 A , B = 830.3 A , C = 830.3 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.3 A , Y = 2.3 A , Z = 2.3 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.32.32.3
M x/y/z361361361
origin x/y/z0.0000.0000.000
length x/y/z830.300830.300830.300
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS361361361
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-298.084340.7599.378
Annotation DetailsThis is a 3D map of Western equine encephalitis virus
Supplement
Sample
NameWestern equine encephalitis virus
Number of Components4
Oligomeric State80 trimers of E1-E2 glycoproteins, 240 copies of capsid protein, vRNA
Component #1: virus - WEEV
Scientific nameWestern equine encephalomyelitis virus
Common NameWEEV
Theoretical Mass52 MDa
Experimental Mass52 MDa
Scientific Name of SpeciesWestern equine encephalomyelitis virus (NCBI Taxonomy: 11039)
Common Name of SpeciesWEEV
EmptyNo
EnvelopedYes
IsolateSPECIES
ClassVIRION
Natural SourceHost Species: Equus caballus (NCBI Taxonomy: 9796)
Host Category: VERTEBRATES
ShellT Number: 4
Experiment
Sample Preparation
Specimen Support DetailsR2/2 Quantifoil grids, C-flat grids
Specimen Stateparticle
BufferDetails: TEN buffer: 0.05 M Tris-HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA
pH: 7.4
Vitrification
Cryogen NameETHANE
MethodBlot for 2s
Temperature80 Kelvin
DetailsVitrification instrument: manual plunger
InstrumentHOMEMADE PLUNGER
Humidity100
Imaging
MicroscopeJEOL 2200FS
Date15-NOV-2007
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 51200 X
Astigmatism300,000x magnification
Nominal Cs2.0 mm
Imaging ModeBRIGHT FIELD
Defocus400 nm - 1850 nm
Energy FilterType: omega , Window: 0-20 eV
Specimen Holder
HolderEucentric, side entry Gatan 626 ( GATAN LIQUID NITROGEN )
Temperature90 Kelvin ( 89 Kelvin - 95 Kelvin )
Camera
DetectorCCD, Kodak SO 163 film
Image Acquisition
Od Range0.9
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images49
Sampling Size2.1 microns
Quant Bit Number16
Processing
Methodsingle particle (icosahedral) reconstruction
3 D reconstruction
AlgorithmPFT
SoftwarePIF
CTF CorrectionEach particle
Resolution By Author12
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections4586
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5210.xml (8.1 KB)
Map dataemd_5210.map.gz (71.2 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5210
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.6 MB
Session file for UCSF-Chimera, 25.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 25.7 KB