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

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Basic information

Entry
Database: EMDB / ID: EMD-10373
TitleCryoEM structure for Turnip mosaic virus (TuMV)
Map dataCryoEM map for Turnip mosaic virus (TuMV)
Sample
  • Virus: Turnip mosaic virus
    • Protein or peptide: Coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Coat protein / Coat protein
Function and homology information
Biological speciesTuMV (virus) / Turnip mosaic 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.
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: 0.03
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10373.png

Downloads & links

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Map

FileDownload / File: emd_10373.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map for Turnip mosaic virus (TuMV)
Voxel sizeX=Y=Z: 1.1 Å
Density
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
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0830.1420.003

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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
    • Protein or peptide: Coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Turnip mosaic virus

SupramoleculeName: Turnip mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12230 / Sci species name: Turnip mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Brassica rapa subsp. rapa (turnip)

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: TuMV (virus) / Strain: Japanese
Molecular weightTheoretical: 24.073395 KDa
SequenceString: PRLKSLTSKM RVPRYEKRVA LNLDHLILYT PEQTDLSNTR STRKQFDTWF EGVMADYELT EDKMQIILNG LMVWCIENGT SPNINGMWV MMDGDDQVEF PIKPLIDHAK PTFRQIMAHF SDVAEAYIEK RNQDRPYMPR YGLQRNLTDM SLARYAFDFY E MTSRTPIR ...String:
PRLKSLTSKM RVPRYEKRVA LNLDHLILYT PEQTDLSNTR STRKQFDTWF EGVMADYELT EDKMQIILNG LMVWCIENGT SPNINGMWV MMDGDDQVEF PIKPLIDHAK PTFRQIMAHF SDVAEAYIEK RNQDRPYMPR YGLQRNLTDM SLARYAFDFY E MTSRTPIR AREAHIQMKA AALRGANNNL FGLDGNVGTT VENTERHTT

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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Details: Model of ssRNA as polyU / Number of copies: 19
Source (natural)Organism: Turnip mosaic virus
Molecular weightTheoretical: 1.485872 KDa
SequenceString:
UUUUU

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 444678 / Software - Name: RELION (ver. 2)
CTF correctionSoftware - Name: CTFFIND (ver. 3)
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)
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: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 194432

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Atomic model buiding 1

Initial modelPDB ID:

5odv


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 270
Output model

PDB-6t34:
Atomic model for Turnip mosaic virus (TuMV)

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