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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, Image by UCSF CHIMERA

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

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

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3j0c

CiteFit

PDB-3j0g

CiteFit

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Fit: output model of fitting

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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.gz ( map file in CCP4 format, 27649 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.07 A/pix
= 205.44 A
192 pix
1.07 A/pix
= 205.44 A
192 pix
1.07 A/pix
= 205.44 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
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 orderXYZ
Dimensions192192192
Origin32-47-297
Limit223144-106
Spacing192192192
Unit CellA= B= C: 205.44 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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-62-62-62
NX/NY/NZ125125125
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
Images
Images
Sample
NameVenezuelan Equine Encephalitis Virus TC-83 Strain
Number of Components4
Oligomeric StateE1-E2-E3-CP complex
Theoretical Mass52MDa
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
Common Name of SpeciesVEEV
NCBI taxonomy11036
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 9796
Host Species: Equus caballus
Host Category: VERTEBRATES
ShellID: 1 , Diameter: 700 A, T Number: 4
Experiment
Sample Preparation
Specimen Support Details400 mesh Quantifoil R 1.2/1.3 copper grids
Specimen Stateparticle
BufferpH: 7
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
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs4.3 mm
Imaging ModeBRIGHT FIELD
Defocus400 nm - 2500 nm
Energy FilterEnergy Filter: Omega Filter
Specimen Holder
HolderEucentric
ModelJEOL 3200FSC CRYOHOLDER
Temperature96 K
Camera
DetectorGENERIC GATAN (4k x 4k)
Distance200
Image Acquisition
#1
Number of Digital Images4000
Details4kx4k CCD Image
Processing
Methodsingle particle reconstruction
3D 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 A
Resolution MethodFSC 0.5
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
PDB Entry ID3N40
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5276.xml (8.4 KB)
Map dataemd_5276.map.gz (1.8 MB)
Imagesemd_5276_1.png (107.1 KB)
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