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- EMDB-2782: Cryo-electron microscopy of Rice dwarf virus virion -

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Basic information

Entry
Database: EMDB / ID: EMD-2782
TitleCryo-electron microscopy of Rice dwarf virus virion
Map data3D reconstruction of Rice dwarf virus virion
Sample
  • Sample: Rice dwarf virus virion
  • Virus: Rice dwarf virus
KeywordsRice dwarf virus / Phytoreovirus / Reoviridae family / Virus particle
Biological speciesRice dwarf virus
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsMiyazaki N / Higashiura A / Higashiura T / Akita F / Hibino H / Omura T / Nakagawa A / Iwasaki K
CitationJournal: J Biochem / Year: 2016
Title: Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes.
Authors: Naoyuki Miyazaki / Akifumi Higashiura / Tomoko Higashiura / Fusamichi Akita / Hiroyuki Hibino / Toshihiro Omura / Atsushi Nakagawa / Kenji Iwasaki /
Abstract: The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 ...The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV.
History
DepositionSep 7, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseNov 25, 2015-
UpdateMar 2, 2016-
Current statusMar 2, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2782.png

Downloads & links

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Map

FileDownload / File: emd_2782.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of Rice dwarf virus virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.93 Å/pix.
x 400 pix.
= 1172. Å		2.93 Å/pix.
x 400 pix.
= 1172. Å		2.93 Å/pix.
x 400 pix.
= 1172. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-11.863731380000001 - 8.87250996
Average (Standard dev.)0.00764933 (±1.01573062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 1172.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.932.932.93
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z1172.0001172.0001172.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-11.8648.8730.008

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Supplemental data

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Sample components

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Entire : Rice dwarf virus virion

EntireName: Rice dwarf virus virion
Components
  • Sample: Rice dwarf virus virion
  • Virus: Rice dwarf virus

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Supramolecule #1000: Rice dwarf virus virion

SupramoleculeName: Rice dwarf virus virion / type: sample / ID: 1000 / Oligomeric state: Icosahedral particle / Number unique components: 1
Molecular weightExperimental: 75 MDa / Theoretical: 75 MDa

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Supramolecule #1: Rice dwarf virus

SupramoleculeName: Rice dwarf virus / type: virus / ID: 1 / NCBI-ID: 10991 / Sci species name: Rice dwarf virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Oryza sativa (Asian cultivated rice) / synonym: PLANTAE(HIGHER PLANTS)
Molecular weightExperimental: 75 MDa / Theoretical: 75 MDa

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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: 6.2 / Details: 100mM Histidine, 10mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateMar 23, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 1034

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