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- EMDB-6713: Inner capsid of Rice Dwarf Virus with T-trimers -

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Basic information

Database: EMDB / ID: 6713
TitleInner capsid of Rice Dwarf Virus with T-trimers
Map data
SampleRice dwarf virus (isolate O):
SourceRice dwarf virus (isolate O)
Methodsingle particle reconstruction / cryo EM / 13.43 Å resolution
AuthorsNakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Murata K / Nakagawa A
CitationJournal: To be published
Title: The second layer shell assembly mechanism of multi-layerd Reoviridae
Authors: Nakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Narita H / Shimizu T / Uehara-Ichiki T / Omura T / Murata K / Nakagawa A
DateDeposition: Mar 14, 2017 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0543
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0543
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_6713.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.88 Å/pix.
= 752. Å
400 pix
1.88 Å/pix.
= 752. Å
400 pix
1.88 Å/pix.
= 752. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.88 Å
Contour Level:0.0543 (by author), 0.0543 (movie #1):
Minimum - Maximum-0.005201788 - 0.1046341
Average (Standard dev.)0.011419812 (0.022113465)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 752.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.881.881.88
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z752.000752.000752.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0050.1050.011

Supplemental data

Sample components

Entire Rice dwarf virus (isolate O)

EntireName: Rice dwarf virus (isolate O) / Number of components: 1

Component #1: virus, Rice dwarf virus (isolate O)

VirusName: Rice dwarf virus (isolate O) / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Rice dwarf virus (isolate O)
Source (natural)Host Species: Rice
Shell #1Name of element: inner shell / T number(triangulation number): 1
Shell #2Name of element: outer shell / T number(triangulation number): 13

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: omega / Energy window: 0-20 eV
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 784
3D reconstructionResolution: 13.43 Å / Resolution method: FSC 0.143 CUT-OFF

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