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- EMDB-5133: 17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like par... -

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Basic information

Entry
Database: EMDB / ID: 5133
Title17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like particle cryomicroscopy structure
KeywordsRHDV / vp60 / vp10 / core-like particles
Samplewild Rabbit Hemorrhagic Disease Viruses core-like particles
Sourcerabbit hemorrhagic disease virus core like particles / virus
Map dataThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus core-like particles.
Methodsingle particle (icosahedral) reconstruction, at 17 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 11, 2009 / Header (metadata) release: Oct 15, 2009 / Map release: Aug 12, 2010 / Last update: Oct 11, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_5133.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.54 A/pix
= 406.4 A
160 pix
2.54 A/pix
= 406.4 A
160 pix
2.54 A/pix
= 406.4 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:1.7 (by author), 1 (movie #1):
Minimum - Maximum-1.95755 - 3.63758
Average (Standard dev.)0.0550003 (0.848303)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
CellA=B=C: 406.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-1.9583.6380.055

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Supplemental data

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Sample components

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Entire wild Rabbit Hemorrhagic Disease Viruses core-like particles

EntireName: wild Rabbit Hemorrhagic Disease Viruses core-like particles
Number of components: 3 / Oligomeric State: icosahedral
MassTheoretical: 7.2 MDa

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Component #1: virus, rabbit hemorrhagic disease virus core like particles

VirusName: rabbit hemorrhagic disease virus core like particles / a.k.a: rabbit hemorrhagic disease virus core like particles / Class: VIROID / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 7.2 MDa
SpeciesSpecies: rabbit hemorrhagic disease virus core like particles / virus
Source (natural)Host Species: Oryctolagus cuniculus / mammal / アナウサギ /
Host category: VERTEBRATES
Shell #1Name of element: S / Diameter: 320 A / T number(triangulation number): 3

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Experimental details

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Sample preparation

Specimen stateparticle
Support film300 mesh holygrid
VitrificationInstrument: NONE / Cryogen name: ETHANE
Method: Embeded 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

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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: GATAN HELIUM / Temperature: 105 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 230 / Sampling size: 12.7 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of class averages: 21 / Number of projections: 895 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: shadow matching method / Software: Eman spider / CTF correction: Each particle / Resolution: 17 A / Resolution method: FSC 0.5

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Atomic model buiding

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

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