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- EMDB-10374: CryoEM structure for viral like particles (VLPs) of Turnip mosaic... -

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Basic information

Entry
Database: EMDB / ID: EMD-10374
TitleCryoEM structure for viral like particles (VLPs) of Turnip mosaic virus (TuMV).
Map dataCryoEM map for viral like particles (VLPs) of Turnip mosaic virus (TuMV)
Sample
  • Virus: Turnip mosaic virus
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein / Genome polyprotein
Function and homology information
Biological speciesTurnip mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsValle M / Cuesta R
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098996-B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2015-66326-P Spain
CitationJournal: Sci Rep / Year: 2019
Title: Structure of Turnip mosaic virus and its viral-like particles.
Authors: Rebeca Cuesta / Carmen Yuste-Calvo / David Gil-Cartón / Flora Sánchez / Fernando Ponz / Mikel Valle /
Abstract: Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide ...Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide representative of the Potyvirus genus, one of most abundant groups of plant viruses, which displays a very wide host range. We have studied by cryoEM the structure of TuMV virions and its viral-like particles (VLPs) to explore the role of the interactions between proteins and RNA in the assembly of the virions. The results show that the CP-RNA interaction is needed for the correct orientation of the CP N-terminal arm, a region that plays as a molecular staple between CP subunits in the fully assembled virion.
History
DepositionOct 10, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10374.png

Downloads & links

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Map

FileDownload / File: emd_10374.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map for viral like particles (VLPs) of Turnip mosaic virus (TuMV)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065 / Movie #1: 0.0065
Minimum - Maximum-0.0013748485 - 0.019731846
Average (Standard dev.)0.0020131795 (±0.0032488457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0010.0200.002

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Supplemental data

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Sample components

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Entire : Turnip mosaic virus

EntireName: Turnip mosaic virus
Components
  • Virus: Turnip mosaic virus

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Supramolecule #1: Turnip mosaic virus

SupramoleculeName: Turnip mosaic virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 12230 / Sci species name: Turnip mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Agrobacterium tumefaciens (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-31 / Number grids imaged: 1 / Average exposure time: 9.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 48625
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Segment selectionNumber selected: 307333 / Software - Name: RELION (ver. 2)
Startup modelType of model: INSILICO MODEL
In silico model: Cylinder with the diameter of the filament.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2)

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