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

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Basic information

Entry
Database: EMDB / ID: EMD-6713
TitleInner capsid of Rice Dwarf Virus with T-trimers
Map data
Sample
  • Virus: Rice dwarf virus (isolate O)
Biological speciesRice dwarf virus (isolate O)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.43 Å
AuthorsNakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Murata K / Nakagawa A
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
DepositionMar 14, 2017-
Header (metadata) releaseJun 27, 2018-
Map releaseJun 27, 2018-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: PDBj / Status: Released

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Structure visualization

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

emd_6713.png

Downloads & links

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Map

FileDownload / File: emd_6713.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 400 pix.
= 752. Å		1.88 Å/pix.
x 400 pix.
= 752. Å		1.88 Å/pix.
x 400 pix.
= 752. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0543 / Movie #1: 0.0543
Minimum - Maximum-0.005201788 - 0.1046341
Average (Standard dev.)0.011419812 (±0.022113465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 752.0 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0050.1050.011

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Supplemental data

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Sample components

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Entire : Rice dwarf virus (isolate O)

EntireName: Rice dwarf virus (isolate O)
Components
  • Virus: Rice dwarf virus (isolate O)

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Supramolecule #1: Rice dwarf virus (isolate O)

SupramoleculeName: Rice dwarf virus (isolate O) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 142805 / Sci species name: Rice dwarf virus (isolate O) / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Rice (Asian cultivated rice)
Virus shellShell ID: 1 / Name: inner shell / T number (triangulation number): 1
Virus shellShell ID: 2 / Name: outer shell / T number (triangulation number): 13

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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: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
81.0 mMNa2HPO4sodium hydrogen phosphate
14.7 mMKH2PO4potassium dihydrogen phosphate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: omega / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: ctffind3
Startup modelType of model: OTHER / Details: A model made by e2initialmodel.py in EMAN2 package
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 13.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 784
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)

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