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- EMDB-10373: CryoEM structure for Turnip mosaic virus (TuMV) -

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Basic information

Database: EMDB / ID: EMD-10373
TitleCryoEM structure for Turnip mosaic virus (TuMV)
Map data
SampleTurnip mosaic virus:
virus / Coat protein / nucleic-acidNucleic acid
Function / homologyPotyvirus coat protein / viral capsid / Coat protein / Coat protein
Function and homology information
Biological speciesTurnip mosaic virus / TuMV (virus)
Methodhelical reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsValle MV / 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.
Validation ReportSummary, Full report, XML, About validation report
DepositionOct 10, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBe / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t34
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6t34
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_10373.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 250 pix.
= 275. Å
1.1 Å/pix.
x 250 pix.
= 275. Å
1.1 Å/pix.
x 250 pix.
= 275. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0832917 - 0.14232388
Average (Standard dev.)0.003384128 (±0.013149834)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 275.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z275.000275.000275.000
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0830.1420.003

Supplemental data

Sample components

Entire Turnip mosaic virus

EntireName: Turnip mosaic virus / Number of components: 3

Component #1: virus, Turnip mosaic virus

VirusName: Turnip mosaic virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Turnip mosaic virus
Source (natural)Host Species: Brassica rapa subsp. rapa (turnip)

Component #2: protein, Coat protein

ProteinName: Coat protein / Number of Copies: 19 / Recombinant expression: No
MassTheoretical: 24.073395 kDa
SourceSpecies: TuMV (virus) / Strain: Japanese

Component #3: nucleic-acid, RNA (5'-R(P*UP*UP*UP*UP*U)-3')

nucleic acidName: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / Class: RNA / Details: Model of ssRNA as polyU / Structure: OTHER / Synthetic: No
MassTheoretical: 1.485872 kDa
SourceSpecies: Turnip mosaic virus

Experimental details

Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4 Å / Delta phi: -40.8 %deg;
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 5ODV
Chain ID: A

Overall bvalue: 270
Output model

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