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- EMDB-1532: Three-dimensional structure of the Grass carp reovirus core. -

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Basic information

Entry
Database: EMDB / ID: EMD-1532
TitleThree-dimensional structure of the Grass carp reovirus core.
Map dataThree-dimensional structure of the grass carp reovirus core.
Sample
  • Sample: Grass carp reovirus core
  • Virus: Grass carp reovirus
KeywordsGrass carp reovirus / aquareovirus / dsRNA virus / 3D structure / reoviridae / cryo-electron microscopy
Biological speciesGrass carp reovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsCheng L / Fang Q / Shah S / Atanasov IC / Zhou ZH
CitationJournal: J Mol Biol / Year: 2008
Title: Subnanometer-resolution structures of the grass carp reovirus core and virion.
Authors: Lingpeng Cheng / Qin Fang / Sanket Shah / Ivo C Atanasov / Z Hong Zhou /
Abstract: Grass carp reovirus (GCRV) is a member of the Aquareovirus genus of the family Reoviridae, a large family of double-stranded RNA (dsRNA) viruses infecting plants, insects, fishes and mammals. We ...Grass carp reovirus (GCRV) is a member of the Aquareovirus genus of the family Reoviridae, a large family of double-stranded RNA (dsRNA) viruses infecting plants, insects, fishes and mammals. We report the first subnanometer-resolution three-dimensional structures of both GCRV core and virion by cryoelectron microscopy. These structures have allowed the delineation of interactions among the over 1000 molecules in this enormous macromolecular machine and a detailed comparison with other dsRNA viruses at the secondary-structure level. The GCRV core structure shows that the inner proteins have strong structural similarities with those of orthoreoviruses even at the level of secondary-structure elements, indicating that the structures involved in viral dsRNA interaction and transcription are highly conserved. In contrast, the level of similarity in structures decreases in the proteins situated in the outer layers of the virion. The proteins involved in host recognition and attachment exhibit the least similarities to other members of Reoviridae. Furthermore, in GCRV, the RNA-translocating turrets are in an open state and lack a counterpart for the sigma1 protein situated on top of the close turrets observed in mammalian orthoreovirus. Interestingly, the distribution and the organization of GCRV core proteins resemble those of the cytoplasmic polyhedrosis virus, a cypovirus and the structurally simplest member of the Reoviridae family. Our results suggest that GCRV occupies a unique structure niche between the simpler cypoviruses and the considerably more complex mammalian orthoreovirus, thus providing an important model for understanding the structural and functional conservation and diversity of this enormous family of dsRNA viruses.
History
DepositionJul 1, 2008-
Header (metadata) releaseJul 2, 2008-
Map releaseApr 1, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1532.gif

Downloads & links

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Map

FileDownload / File: emd_1532.map.gz / Format: CCP4 / Size: 728.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree-dimensional structure of the grass carp reovirus core.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 366 pix.
= 424.56 Å		1.16 Å/pix.
x 731 pix.
= 847.96 Å		1.16 Å/pix.
x 731 pix.
= 847.96 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: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 3
Minimum - Maximum-9.15338 - 13.8085
Average (Standard dev.)0.0597168 (±1.38766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions731731366
Spacing731731366
CellA: 847.96 Å / B: 847.96 Å / C: 424.56 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z731731366
origin x/y/z0.0000.0000.000
length x/y/z847.960847.960424.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS731731366
D min/max/mean-9.15313.8090.060

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Supplemental data

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Sample components

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Entire : Grass carp reovirus core

EntireName: Grass carp reovirus core
Components
  • Sample: Grass carp reovirus core
  • Virus: Grass carp reovirus

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Supramolecule #1000: Grass carp reovirus core

SupramoleculeName: Grass carp reovirus core / type: sample / ID: 1000 / Number unique components: 5

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Supramolecule #1: Grass carp reovirus

SupramoleculeName: Grass carp reovirus / type: virus / ID: 1 / Name.synonym: aquareovirus / NCBI-ID: 128987 / Sci species name: Grass carp reovirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: aquareovirus
Host (natural)Organism: Ctenopharyngodon idella (grass carp) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: GCRV core / Diameter: 810 Å / T number (triangulation number): 1

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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

Concentration2.5 mg/mL
BufferpH: 7.5
Details: 10 mM PBS, 137mM NaCL, 2.7mM KCl, 8.1mM Na2HP04, 1.5mM KH2PO4
GridDetails: 400 mesh
VitrificationCryogen name: NITROGEN / Instrument: OTHER
Method: Blot for 1 seconds before plunging. The sample was quickly plunged into a bath of liquid ethane cooled by liquid nitrogen.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 129480 / Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 20 e/Å2 / Bits/pixel: 32
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each microscoph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMIRS / Number images used: 3697
DetailsThe particles were selected using an automatic selection program and verified manually.

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Atomic model buiding 1

Initial modelPDB ID:

1ej6


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: E
SoftwareName: UCSF Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. Automatically done by UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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