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- EMDB-2054: Electron cryo-microscopy of Mud Crab Reovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-2054
TitleElectron cryo-microscopy of Mud Crab Reovirus
Map dataReconstruction of native Mud Crab Reovirus (MCRV)
Sample
  • Sample: Mud Crab Reovirus (MCRV)
  • Virus: Mud Crab Reovirus
KeywordsMud Crab Reovirus
Biological speciesMud Crab Reovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 13.8 Å
AuthorsZengwei H / Xiexiong D / Yinyin L / Hongjun S / Kunpeng L / Zhixun G / Peirui Z / Haidong X / Jianguo H / Qinfen Z / Shaoping W
CitationJournal: Virus Res / Year: 2012
Title: Structural insights into the classification of Mud Crab Reovirus.
Authors: Zengwei Huang / Xiexiong Deng / Yinyin Li / Hongjun Su / Kunpeng Li / Zhixun Guo / Peirui Zheng / Haidong Xu / Jianguo He / Qinfen Zhang / Shaoping Weng /
Abstract: Cryo-electron microscopy was applied to analyze mud crab reovirus (MCRV), which causes 'sleeping disease' in mud crab, Scylla serrata, a marine species cultured in China. We present here the three ...Cryo-electron microscopy was applied to analyze mud crab reovirus (MCRV), which causes 'sleeping disease' in mud crab, Scylla serrata, a marine species cultured in China. We present here the three dimensional structure of MCRV at 13.8Å resolution. The outer capsid shell is composed of 260 trimers with complete T=13 icosahedral symmetry. A major difference between MCRV and previously reported aquareoviruses is that it lacks a pentameric turret structure. These results together with recently published molecular biological evidence (Deng et al., 2012) indicate that, from a structural perspective, MCRV should be classified as a new member of the family Reoviridae.
History
DepositionMar 17, 2012-
Header (metadata) releaseMar 23, 2012-
Map releaseSep 26, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2054.png

Downloads & links

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Map

FileDownload / File: emd_2054.map.gz / Format: CCP4 / Size: 36.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of native Mud Crab Reovirus (MCRV)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 135 pix.
= 364.5 Å		2.7 Å/pix.
x 270 pix.
= 729. Å		2.7 Å/pix.
x 270 pix.
= 729. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.0 / Movie #1: 0.1
Minimum - Maximum-2.03657198 - 4.01148891
Average (Standard dev.)0.49377689 (±1.37695026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270135
Spacing270270135
CellA: 729.0 Å / B: 729.0 Å / C: 364.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z270270135
origin x/y/z0.0000.0000.000
length x/y/z729.000729.000364.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270135
D min/max/mean-2.0374.0110.494

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Supplemental data

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Sample components

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Entire : Mud Crab Reovirus (MCRV)

EntireName: Mud Crab Reovirus (MCRV)
Components
  • Sample: Mud Crab Reovirus (MCRV)
  • Virus: Mud Crab Reovirus

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Supramolecule #1000: Mud Crab Reovirus (MCRV)

SupramoleculeName: Mud Crab Reovirus (MCRV) / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1

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Supramolecule #1: Mud Crab Reovirus

SupramoleculeName: Mud Crab Reovirus / type: virus / ID: 1 / Name.synonym: Mud Crab Reovirus / Sci species name: Mud Crab Reovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Mud Crab Reovirus
Host (natural)Organism: Scylla serrata (giant mud crab) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 724 Å / T number (triangulation number): 13

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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

BufferpH: 7.2 / Details: 0.1M PBS
GridDetails: R1.2/1.3 Quantifoil grids(200mesh) with thin carbon film
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: freezed by manual / Method: blot about 5 seconds by manual before plunging

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Electron microscopy

MicroscopeJEOL 2010
TemperatureMin: 100 K / Max: 103 K / Average: 102 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification
DetailsMiminum dose illumination (MDS model)
DateJan 12, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 6.5 µm / Number real images: 100 / Average electron dose: 18 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 46900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected by EMAN boxer programms.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 13.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 4020

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