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10.5 angstrom of Rabbit Hemorrhagic Disease Virus(RHDV)cryomicroscopy structure

by single particle reconstruction, at 10.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.15, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.15, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5131
Title10.5 angstrom of Rabbit Hemorrhagic Disease Virus(RHDV)cryomicroscopy structure
MapThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus
SampleWild Rabbit Hemorrhagic Disease Viruses
KeywordsRHDV, vp60, vp10
AuthorsHu Z, Tian X, Zhai Y, Xu W, Zheng D, Sun F
DateDeposition: 2009-10-08, Header release: 2009-10-15, Map release: 2010-08-12, Last update: 2011-01-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.15, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.15, Made by UCSF CHIMERA

Supplemental images

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

EMDB-5133
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1933

EMDB-1939

EMDB-1935

EMDB-1934

EMDB-1936

EMDB-1938
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProtein Cell, Vol. 1, Issue 1, Page 48-58, Year 2010
TitleCryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus.
AuthorsZhongjun Hu, Xiaojuan Tian, Yujia Zhai, Wei Xu, Dong Zheng, Fei Sun
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
KeywordsAmino Acid Sequence, Animals, Caliciviridae Infections (virology), China, Cryoelectron Microscopy, Hemorrhagic Disease Virus, Rabbit (ultrastructure), Molecular Sequence Data, Rabbits, Sequence Alignment, Viral Structural Proteins (chemistry), Virion (ultrastructure), viral protein 60, rabbit hemorrhagic disease virus
LinksDOI: 10.1007/s13238-010-0007-0, PubMed: 21203997
Map
FileEMD-5131.map ( map file in CCP4 format, 32002 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:1.15 (by author), 1.15 (movie #1):
Minimum - Maximum: -4.19832 - 5.0759
Average (Standard dev.): -0.012319 (0.714993)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 200 200 200
Origin : -100 -100 -100
Limit : 99 99 99
Spacing : 200 200 200
Unit CellA = 508 A , B = 508 A , C = 508 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.54 A , Y = 2.54 A , Z = 2.54 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.542.542.54
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z508.000508.000508.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-4.1985.076-0.012
Annotation DetailsThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus
Supplement
Sample
NameWild Rabbit Hemorrhagic Disease Viruses
Number of Components3
Oligomeric StateIcosahedral
Theoretical Mass13.0 MDa
Component #1: virus - rabbit hemorrhagic disease viruses
Scientific namerabbit hemorrhagic disease viruses
Theoretical Mass1300 MDa
Scientific Name of Speciesrabbit hemorrhagic disease viruses
Common Name of Speciesrabbit hemorrhagic disease viruses
EmptyNo
EnvelopedNo
IsolateSPECIES
ClassVIRION
Natural SourceHost Species: Oryctolagus cuniculus (NCBI Taxonomy: 9986)
Host Category: VERTEBRATES
ShellDiameter: 430 A
T Number: 3
Experiment
Sample Preparation
Specimen Support Details300 mesh holygrid
Specimen Stateparticle
Vitrification
MethodManually blotting the grids with filter paper and then plunging into liquid ethane cooled by liquid nitrogen
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 20
Electron Gun
Electron SourceLAB6
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X,
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 4000 nm
Specimen Holder
HolderEucentric ( SIDE ENTRY, EUCENTRIC )
Temperature105 Kelvin
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images230
Sampling Size12.7 microns
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3 D reconstruction
SoftwareEman, Spider
CTF CorrectionEach particle
Resolution By Author10.5
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections15890
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body
Softwarechimera
Refinement Protocolrigid body
Refinement SpaceREAL
Download
Data from EMDB
Header (meta data in XML format)emd-5131.xml (7.2 KB)
Map dataemd_5131.map.gz (27.1 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5131
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.1 KB