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- EMDB-6989: Inner capsid of Rice Dwarf Virus with T-trimers (Full particle) -

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Basic information

Entry
Database: EMDB / ID: 6989
TitleInner capsid of Rice Dwarf Virus with T-trimers (Full particle)
Map data
SampleRice dwarf virus:
virus
SourceRice dwarf virus
Methodsingle particle reconstruction / cryo EM / 6.4 Å resolution
AuthorsNakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Narita H / Murata K / Nakagawa A
CitationJournal: Structure / Year: 2018
Title: An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism.
Authors: Yusuke Nakamichi / Naoyuki Miyazaki / Kenta Tsutsumi / Akifumi Higashiura / Hirotaka Narita / Kazuyoshi Murata / Atsushi Nakagawa
Abstract: Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric ...Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions.
DateDeposition: Jun 28, 2018 / Header (metadata) release: Sep 19, 2018 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6989.map.gz (map file in CCP4 format, 702465 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
560 pix
1.39 Å/pix.
= 778.4 Å
560 pix
1.39 Å/pix.
= 778.4 Å
560 pix
1.39 Å/pix.
= 778.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.034 (by author), 0.034 (movie #1):
Minimum - Maximum-0.021798994 - 0.13807411
Average (Standard dev.)0.0013808296 (0.007514493)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions560560560
Origin0.00.00.0
Limit559.0559.0559.0
Spacing560560560
CellA=B=C: 778.39996 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z778.400778.400778.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0220.1380.001

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Supplemental data

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Sample components

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Entire Rice dwarf virus

EntireName: Rice dwarf virus / Number of components: 1

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Component #1: virus, Rice dwarf virus

VirusName: Rice dwarf virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Rice dwarf virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47000.0 X (nominal) / Cs: 0.1 mm / Imaging mode: BRIGHT FIELD / Defocus: -1000.0 - -1200.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 90.0 - 95.0 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2804 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 10122
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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