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

by single particle (icosahedral) reconstruction, at 10.5 A resolution

Movie

Orientation:

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

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

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

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

Cite: data citing same article

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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.gz ( map file in CCP4 format, 31251 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
2.54 A/pix
= 508. A
200 pix
2.54 A/pix
= 508. A
200 pix
2.54 A/pix
= 508. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
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 orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
Unit CellA= B= C: 508 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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
Images
Images
Sample
NameWild Rabbit Hemorrhagic Disease Viruses
Number of Components3
Oligomeric StateIcosahedral
Theoretical Mass13MDa
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 SourceNCBI taxonomy: 9986
Host Species: Oryctolagus cuniculus
Host Category: VERTEBRATES
ShellID: 1 , Diameter: 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
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 4000 nm
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Temperature105 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images230
Sampling Size12.7
Quant Bit Number16
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
SoftwareEman, Spider
CTF CorrectionEach particle
Resolution By Author10.5 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections15890
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body
Softwarechimera
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID2GH8
Download
Data from EMDB
Header (meta data in XML format)emd-5131.xml (7.3 KB)
Map dataemd_5131.map.gz (27.1 MB)
Imagesemd_5131_1.jpg (121.7 KB)
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