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- EMDB-5131: 10.5 angstrom of Rabbit Hemorrhagic Disease Virus(RHDV)cryomicros... -

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Basic information

Entry
Database: EMDB / ID: 5131
Title10.5 angstrom of Rabbit Hemorrhagic Disease Virus(RHDV)cryomicroscopy structure
KeywordsRHDV / vp60 / vp10
SampleWild Rabbit Hemorrhagic Disease Viruses
Sourcerabbit hemorrhagic disease viruses / virus
Map dataThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus
Methodsingle particle (icosahedral) reconstruction, at 10.5 A resolution
AuthorsHu Z / Tian X / Zhai Y / Xu W / Zheng D / Sun F
CitationProtein Cell, 2010, 1, 48-58

Protein Cell, 2010, 1, 48-58 StrPapers
Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus.
Zhongjun Hu / Xiaojuan Tian / Yujia Zhai / Wei Xu / Dong Zheng / Fei Sun

DateDeposition: Oct 8, 2009 / Header (metadata) release: Oct 15, 2009 / Map release: Aug 12, 2010 / Last update: Oct 8, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.15
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1.15
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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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.

Voxel sizeX=Y=Z: 2.54 A
Density
Contour Level:1.15 (by author), 1.15 (movie #1):
Minimum - Maximum-4.19832 - 5.0759
Average (Standard dev.)-0.012319 (0.714993)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 508 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-4.1985.076-0.012

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Supplemental data

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Sample components

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Entire Wild Rabbit Hemorrhagic Disease Viruses

EntireName: Wild Rabbit Hemorrhagic Disease Viruses / Number of components: 3 / Oligomeric State: Icosahedral
MassTheoretical: 13 MDa

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Component #1: virus, rabbit hemorrhagic disease viruses

VirusName: rabbit hemorrhagic disease viruses / a.k.a: rabbit hemorrhagic disease viruses / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 1.3GDa
SpeciesSpecies: rabbit hemorrhagic disease viruses / virus
Source (natural)Host Species: Oryctolagus cuniculus / mammal / アナウサギ /
Host category: VERTEBRATES

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Experimental details

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Sample preparation

Specimen stateparticle
Support film300 mesh holygrid
VitrificationInstrument: NONE / Cryogen name: ETHANE
Method: Manually blotting the grids with filter paper and then plunging into liquid ethane cooled by liquid nitrogen

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC / Temperature: 105 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 230 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 12.7 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 15890 / Applied symmetry: I (icosahedral)
3D reconstructionSoftware: Eman, Spider / CTF correction: Each particle / Resolution: 10.5 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: chimera / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 2GH8

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