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Cryo-EM of Rift Valley fever virus

by single particle (icosahedral) reconstruction, at 27 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 7.3, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 7.3, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5124
TitleCryo-EM of Rift Valley fever virus
Mapthis is RVFV map in 2-fold orientation
SampleRift Valley fever virus, RVFV vaccine strain MP-12
Keywordscryo-electron microscopy, single particle averaging, Rift valley fever, bunyaviridae, inter-capsomer contacts
AuthorsSherman MB, Freiberg AN, Holbrook AM, Watowich SJ
DateDeposition: 2009-07-20, Header release: 2009-07-24, Map release: 2009-07-24, Last update: 2011-07-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 7.3, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 7.3, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleVirology, Vol. 387, Issue 1, Page 11-5, Year 2009
TitleSingle-particle cryo-electron microscopy of Rift Valley fever virus.
AuthorsMichael B Sherman, Alexander N Freiberg, Michael R Holbrook, Stanley J Watowich
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0647, USA.
KeywordsCryoelectron Microscopy (methods), Glycoproteins (metabolism), Image Processing, Computer-Assisted, Membrane Lipids (metabolism), Rift Valley fever virus (ultrastructure), Viral Envelope Proteins (metabolism), viral envelope lipids
LinksDOI: 10.1016/j.virol.2009.02.038, PubMed: 19304307, PMC: PMC2673237
Citation - #1
ArticleJ.VIROL., Vol. 82, Page 10341-10348, Year 2008
TitleThree-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography
AuthorsFreiberg AN, Sherman MB, Morais MC, Holbrook MR, Watowich SJ
Map
Fileemd_5124.map.gz ( map file in CCP4 format, 358337 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
451 pix
3 A/pix
= 1353. A
451 pix
3 A/pix
= 1353. A
451 pix
3 A/pix
= 1353. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:6 (by author), 7.3 (movie #1):
Minimum - Maximum: -26.2832 - 37.4125
Average (Standard dev.): 0.675954 (6.08815)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions451451451
Origin-225-225-225
Limit225225225
Spacing451451451
Unit CellA= B= C: 1353 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z333
M x/y/z451451451
origin x/y/z0.0000.0000.000
length x/y/z1353.0001353.0001353.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS451451451
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-26.28337.4120.676
Annotation Detailsthis is RVFV map in 2-fold orientation
Supplement
Images
Images
Sample
NameRift Valley fever virus, RVFV vaccine strain MP-12
Number of Components8
Oligomeric Statesingle virions
Detailsmonodisperse sample
Component #1: virus - RVFV
Scientific nameRift Valley fever virus
Common NameRVFV
Details100 nm particles
Scientific Name of SpeciesRift Valley fever virus
Common Name of SpeciesRVFV
NCBI taxonomy11588
EmptyNo
EnvelopedYes
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: VERTEBRATES
ShellID: 1 , Diameter: 1000 A, T Number: 12
Experiment
Sample Preparation
Specimen Conc0.1 mg/ml
Specimen Support Details200 mesh copper Qauntifoil grids
Specimen Stateparticle
BufferDetails: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA
pH: 7.2
Vitrification
Methodblot 2 sec before plunging
Cryogen NameETHANE
DetailsVitrification instrument: pneumatic plunger
Humidity80
InstrumentHOMEMADE PLUNGER
Temperature95 Kelvin
Imaging
MicroscopeJEOL 2200FS
Date01-Nov-2007
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 40000, Calibrated: 40200
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus700 nm - 3700 nm
Energy FilterEnergy Filter: omega , Energy Window: 0-20 eV
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature99 K ( 99 - 99 K)
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Image Acquisition
Number of Digital Images93
Sampling Size14
Quant Bit Number16
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmPFT
SoftwarePFT
CTF CorrectionEach particle
DetailsFinal map calculated from 108 particles
Resolution By Author27 A
Resolution MethodFSC
Single Particle
Number of Projections108
Number of Class Averages1
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5124.xml (8.5 KB)
Map dataemd_5124.map.gz (144.3 MB)
Imagesemd_5124_1.png (347.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5124
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 25.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 25.6 KB