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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: EMD-6989
TitleInner capsid of Rice Dwarf Virus with T-trimers (Full particle)
Map data
Sample
  • Virus: Rice dwarf virus
Biological speciesRice dwarf virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsNakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Narita H / Murata K / Nakagawa A
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25251009 Japan
Japan Agency for Medical Research and Development (AMED) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Structure / Year: 2019
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.
History
DepositionJun 28, 2018-
Header (metadata) releaseSep 19, 2018-
Map releaseJan 16, 2019-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: PDBj / Status: Released

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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

emd_6989.png

Downloads & links

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Map

FileDownload / File: emd_6989.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.021798994 - 0.13807411
Average (Standard dev.)0.0013808296 (±0.007514493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 778.39996 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ352352352
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
Components
  • Virus: Rice dwarf virus

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Supramolecule #1: Rice dwarf virus

SupramoleculeName: Rice dwarf virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10991 / Sci species name: Rice dwarf virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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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
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 90.0 K / Max: 95.0 K
Specialist opticsPhase plate: VOLTA PHASE PLATE / Spherical aberration corrector: CEOS Cs-corrector
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-30 / Number grids imaged: 1 / Number real images: 2804 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: -1.2 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 15499
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1uf2


Details: P8 trimers corresponding to P, Q, R and S positions and P7 fragments were removed.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 10122
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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