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17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like particle cryomicroscopy structure

by single particle reconstruction, at 17 A resolution

Movie

Orientation:

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

#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5133
Title17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like particle cryomicroscopy structure
MapThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus core-like particles.
Samplewild Rabbit Hemorrhagic Disease Viruses core-like particles
KeywordsRHDV, vp60, vp10, core-like particles
AuthorsHu Z, Tian X, Zhai Y, Xu W, Zheng D, Sun F
DateDeposition: 2009-10-11, 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, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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EMDB-5131
Cite

Cite: data citing same article

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Diagram

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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-5133.map ( map file in CCP4 format, 16386 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:1.7 (by author), 1 (movie #1):
Minimum - Maximum: -1.95755 - 3.63758
Average (Standard dev.): 0.0550003 (0.848303)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 160 160 160
Origin : -80 -80 -80
Limit : 79 79 79
Spacing : 160 160 160
Unit CellA = 406.4 A , B = 406.4 A , C = 406.4 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/z160160160
origin x/y/z0.0000.0000.000
length x/y/z406.400406.400406.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.9583.6380.055
Annotation DetailsThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus core-like particles.
Supplement
Sample
Namewild Rabbit Hemorrhagic Disease Viruses core-like particles
Number of Components3
Oligomeric Stateicosahedral
Theoretical Mass7.2 MDa
Component #1: virus - rabbit hemorrhagic disease virus core like particles
Scientific namerabbit hemorrhagic disease virus core like particles
Theoretical Mass7.2 MDa
Scientific Name of Speciesrabbit hemorrhagic disease virus core like particles
Common Name of Speciesrabbit hemorrhagic disease virus core like particles
EmptyNo
EnvelopedNo
IsolateSPECIES
ClassVIROID
Natural SourceHost Species: Oryctolagus cuniculus (NCBI Taxonomy: 9986)
Host Category: VERTEBRATES
ShellDiameter: 320 A
Name Element: S
T Number: 3
Experiment
Sample Preparation
Specimen Support Details300 mesh holygrid
Specimen Stateparticle
Vitrification
MethodEmbeded in thin layer of vitreous ice on freshly carbon-coated home-made holey EM grid by manually 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 ( GATAN HELIUM )
Temperature105 Kelvin
Camera
DetectorKodak SO163 film
Image Acquisition
Number of Digital Images230
Sampling Size12.7 microns
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmshadow matching method
SoftwareEman spider
CTF CorrectionEach particle
Resolution By Author17
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages21
Number of Projections895
Atomic Model Fitting
Model #0
Target Criteriacorrelation coefficient
DetailsProtocol: Rigid Body
Softwarechimera
Refinement Protocolrigid body
Refinement SpaceREAL
Download
Data from EMDB
Header (meta data in XML format)emd-5133.xml (7.6 KB)
Map dataemd_5133.map.gz (11.1 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5133
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.4 KB