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4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus

by single particle reconstruction, at 4.8 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 6, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 6, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0c, Surface level: 6, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5276
Title4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus
MapThis is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map.
SampleVenezuelan Equine Encephalitis Virus TC-83 Strain
Keywordsalphavirus, bioweapon, cryoEM, modeling, VEEV
AuthorsZhang R, Hryc CF, Cong Y, Liu X, Jakana J, Gorchakov R, Baker ML, Weaver SC, Chiu W
DateDeposition: 2011-04-15, Header release: 2011-04-19, Map release: 2011-08-16, Last update: 2012-09-19
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 6, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 6, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0c, Surface level: 6, Made by UCSF CHIMERA

Supplemental images

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

PDB-3j0c
CiteFit

PDB-3j0g
CiteFit

EMDB-5275
Cite

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)

Diagram

PDB-3izd

EMDB-2263

EMDB-2260
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 30, Issue 18, Page 3854-63, Year 2011
Title4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus.
AuthorsRui Zhang, Corey F Hryc, Yao Cong, Xiangan Liu, Joanita Jakana, Rodion Gorchakov, Matthew L Baker, Scott C Weaver, Wah Chiu
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA.
KeywordsAnimals, Cryoelectron Microscopy, Encephalitis Virus, Venezuelan Equine (ultrastructure), Horses, Models, Molecular, Viral Proteins (ultrastructure), Viral Vaccines, Virion (ultrastructure), Virulence
LinksDOI: 10.1038/emboj.2011.261, PubMed: 21829169, PMC: PMC3173789
Map
FileEMD-5276.map ( map file in CCP4 format, 28313 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:6 (by author), 6 (movie #1):
Minimum - Maximum: -13.58756733 - 32.44748688
Average (Standard dev.): -0.00455169 (0.93261677)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 192 192 192
Origin : -47 32 -297
Limit : 144 223 -106
Spacing : 192 192 192
Unit CellA = 205.44 A , B = 205.44 A , C = 205.44 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 1.07 A , Y = 1.07 A , Z = 1.07 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.071.071.07
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z205.440205.440205.440
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-4732-297
NC/NR/NS192192192
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-13.58832.447-0.005
Annotation DetailsThis is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map.
Supplement
Sample
NameVenezuelan Equine Encephalitis Virus TC-83 Strain
Number of Components4
Oligomeric StateE1-E2-E3-CP complex
Theoretical Mass52 MDa
DetailsThe viruses were purified from infected Baby hamster kidney (BHK) cells
Component #1: virus - VEEV
Scientific nameVenezuelan equine encephalitis virus
Common NameVEEV
Theoretical Mass52 MDa
Scientific Name of SpeciesVenezuelan equine encephalitis virus (NCBI Taxonomy: 11036)
Common Name of SpeciesVEEV
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceHost Species: Equus caballus (NCBI Taxonomy: 9796)
Host Category: VERTEBRATES
ShellDiameter: 700 A
T Number: 4
Experiment
Sample Preparation
Specimen Support Details400 mesh Quantifoil R 1.2/1.3 copper grids
Specimen Stateparticle
BufferpH: 7.0
Vitrification
Method2 blots, each blot 2 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature100 Kelvin
Imaging
MicroscopeJEOL 3200FSC
Date09-APR-2008
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose18 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 100000 X,
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs4.3 mm
Imaging ModeBRIGHT FIELD
Defocus400 nm - 2500 nm
Energy FilterType: Omega Filter , Window:
Specimen Holder
HolderEucentric ( JEOL 3200FSC CRYOHOLDER )
Temperature96 Kelvin
Camera
DetectorGatan 4kx4k CCD Camera
Distance200
Image Acquisition
Number of Digital Images4000
Details4kx4k CCD Image
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmprojection matching
SoftwareEMAN
CTF CorrectionEach frame
DetailsThis is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map
Resolution By Author4.8
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages1000
Number of Projections37000
DetailsThe virus particles were automatically boxed out using ethan, among which around 10,000 particles contained continuous carbon film.
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body
Refinement Protocolrigid body
Refinement SpaceREAL
Fitted Coordinate
PDB entry ID

PDB-3j0c

PDB-3j0g
Download
Data from EMDB
Header (meta data in XML format)emd-5276.xml (8.4 KB)
Map dataemd_5276.map.gz (1.8 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5276
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 28.7 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 3.2 MB