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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: EMD-5131
Title10.5 angstrom of Rabbit Hemorrhagic Disease Virus(RHDV)cryomicroscopy structure
Map dataThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus
Sample
  • Sample: Wild Rabbit Hemorrhagic Disease Viruses
  • Virus: rabbit hemorrhagic disease viruses
KeywordsRHDV / vp60 / vp10
Biological speciesrabbit hemorrhagic disease viruses
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsHu Z / Tian X / Zhai Y / Xu W / Zheng D / Sun F
CitationJournal: Protein Cell / Year: 2010
Title: Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus.
Authors: Zhongjun Hu / Xiaojuan Tian / Yujia Zhai / Wei Xu / Dong Zheng / Fei Sun /
Abstract: Rabbit hemorrhagic disease was described in China in 1984 and can cause hemorrhagic necrosis of the liver within two or three days after infection. The etiological agent, rabbit hemorrhagic disease ...Rabbit hemorrhagic disease was described in China in 1984 and can cause hemorrhagic necrosis of the liver within two or three days after infection. The etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus in the Caliciviridae family. Compared to other calicivirus, such as rNV and SMSV, the structure of Lagovirus members is not well characterized. In this report, structures of two types of wild RHDV particles, the intact virion and the core-like particle (CLP), were reconstructed by cryo-electron microscopy at 11 &0A and 17 &0A, respectively. This is the first time the 3D structure of wild caliciviruses CLP has been provided, and the 3D structure of intact RHDV virion is the highest resolution structure in Lagovirus. Comparison of the intact virion and CLP structures clearly indicated that CLP was produced from the intact virion with the protrusion dissociated. In contrast with the crystal structures of recombinant Norovirus and San Miguel sea lion virus, the capsomers of RHDV virion exhibited unique structural features and assembly modes. Both P1 and P2 subdomains have interactions inside the AB capsomer, while only P2 subdomains have interaction inside CC capsomer. The pseudo atomic models of RHDV capsomers were constructed by homology modeling and density map fitting, and the rotation of RHDV VP60 P domain with respect to its S domain, compared with SMSV, was observed. Collectively, our cryo-electron microscopic studies of RHDV provide close insight into the structure of Lagovirus, which is important for functional analysis and better vaccine development in the future.
History
DepositionOct 8, 2009-
Header (metadata) releaseOct 15, 2009-
Map releaseAug 12, 2010-
UpdateJan 10, 2011-
Current statusJan 10, 2011Processing site: RCSB / Status: Released

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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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5131_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5131.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 200 pix.
= 508. Å		2.54 Å/pix.
x 200 pix.
= 508. Å		2.54 Å/pix.
x 200 pix.
= 508. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.15 / Movie #1: 1.15
Minimum - Maximum-4.19832 - 5.0759
Average (Standard dev.)-0.012319 (±0.714993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 508 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: Wild Rabbit Hemorrhagic Disease Viruses
  • Virus: rabbit hemorrhagic disease viruses

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Supramolecule #1000: Wild Rabbit Hemorrhagic Disease Viruses

SupramoleculeName: Wild Rabbit Hemorrhagic Disease Viruses / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 3
Molecular weightTheoretical: 13.0 MDa

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Supramolecule #1: rabbit hemorrhagic disease viruses

SupramoleculeName: rabbit hemorrhagic disease viruses / type: virus / ID: 1 / Name.synonym: rabbit hemorrhagic disease viruses / Sci species name: rabbit hemorrhagic disease viruses / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: rabbit hemorrhagic disease viruses
Host (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: VERTEBRATES
Molecular weightTheoretical: 1300 MDa
Virus shellShell ID: 1 / Diameter: 430 Å / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

GridDetails: 300 mesh holygrid
VitrificationCryogen name: ETHANE / Instrument: OTHER
Method: Manually blotting the grids with filter paper and then plunging into liquid ethane cooled by liquid nitrogen

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Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 105 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Number real images: 230 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

CTF correctionDetails: Each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Eman, Spider / Number images used: 15890

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Atomic model buiding 1

Initial modelPDB ID:

2gh8

SoftwareName: chimera
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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