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- EMDB-10003: CryoEM structure of wild-type Turnip Yellows Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-10003
TitleCryoEM structure of wild-type Turnip Yellows Virus
Map datasharpened map
Sample
  • Virus: Beet western yellows virus-FL1
    • Protein or peptide: Major coat protein
    • Protein or peptide: Minor capsid protein P3-RTD
Keywordsvirus
Function / homology
Function and homology information


host cell plasmodesma / host cell periplasmic space / T=3 icosahedral viral capsid / viral capsid / structural molecule activity
Similarity search - Function
Potato leaf roll virus readthrough protein / Potato leaf roll virus readthrough protein / Luteovirus group 1 coat protein / Luteovirus coat protein
Similarity search - Domain/homology
Major capsid protein / Readthrough protein P3-RTD
Similarity search - Component
Biological speciesBeet western yellows virus-FL1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsTrapani S / Lai Kee Him J / Hoh F / Brault V / Bron P
Funding support France, 1 items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05 France
CitationJournal: Virology / Year: 2025
Title: Structure of the turnip yellows virus particles.
Authors: Joséphine Lai-Kee-Him / Stefano Trapani / Sylvaine Boissinot / Catherine Reinbold / Chloé Fallet / Aurélie Ancelin / François Lecorre / François Hoh / Véronique Ziegler-Graff / ...Authors: Joséphine Lai-Kee-Him / Stefano Trapani / Sylvaine Boissinot / Catherine Reinbold / Chloé Fallet / Aurélie Ancelin / François Lecorre / François Hoh / Véronique Ziegler-Graff / Véronique Brault / Patrick Bron /
Abstract: Turnip yellows virus (TuYV) is a plant virus infecting important crops such as oilseed rape. TuYV is phloem-restricted and transmitted by aphids. The capsid contains two subunit types: the major ...Turnip yellows virus (TuYV) is a plant virus infecting important crops such as oilseed rape. TuYV is phloem-restricted and transmitted by aphids. The capsid contains two subunit types: the major capsid protein (CP) and a minor component (RTP∗) which arises from the C-terminal cleavage of a readthrough product (RTP). RTP∗ contains the CP sequence fused with a structured domain, denoted RTD, which is a key determinant of virus transmission. Though both CP and RTP∗ are involved in virus movement and aphid transmission, how RTP∗ is incorporated into the capsid is poorly understood. We present here the structural characterisation, by immunogold labelling and 3D cryo-EM, of the wild-type TuYV and a mutant whose capsid contains the CP only. We show that incorporation of RTP∗ does not impair the capsid structure, and the RTD does not adopt well-defined positions at the capsid surface. The number of incorporated RTP∗s suggests a random insertion.
History
DepositionMay 24, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseJul 8, 2020-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0068
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0068
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10003.png

Downloads & links

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Map

FileDownload / File: emd_10003.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 380 pix.
= 465.5 Å		1.23 Å/pix.
x 380 pix.
= 465.5 Å		1.23 Å/pix.
x 380 pix.
= 465.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.225 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0068 / Movie #1: 0.0068
Minimum - Maximum-0.030734144 - 0.046095405
Average (Standard dev.)0.00002126763 (±0.0025312488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 465.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2251.2251.225
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z465.500465.500465.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0310.0460.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_10003_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_10003_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1 map

Fileemd_10003_half_map_1.map
Annotationhalf_1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 map

Fileemd_10003_half_map_2.map
Annotationhalf_2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Beet western yellows virus-FL1

EntireName: Beet western yellows virus-FL1
Components
  • Virus: Beet western yellows virus-FL1
    • Protein or peptide: Major coat protein
    • Protein or peptide: Minor capsid protein P3-RTD

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Supramolecule #1: Beet western yellows virus-FL1

SupramoleculeName: Beet western yellows virus-FL1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12043 / Sci species name: Beet western yellows virus-FL1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: capsid / T number (triangulation number): 3

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Macromolecule #1: Major coat protein

MacromoleculeName: Major coat protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Beet western yellows virus-FL1
SequenceString: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD ...String:
MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD VAEDQFRILY KG NGSSSIA GSFRITIKCQ FHNPK

UniProtKB: Major capsid protein

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Macromolecule #2: Minor capsid protein P3-RTD

MacromoleculeName: Minor capsid protein P3-RTD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Beet western yellows virus-FL1
SequenceString: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD ...String:
MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD VAEDQFRILY KG NGSSSIA GSFRITIKCQ FHNPKYVDEE PGPSPGPSPS PQPTPQKKYR FIVYTGVPVT RIM AQSTDD AISLYDMPSQ RFRYIEDENM NWTNLDSRWY SQNSLKAIPM IIVPVPQGEW TVEI SMEGY QPTSSTTDPN KDKQDGLIAY NDDLSEGWNV GIYNNVEITN NKADNTLKYG HPDME LNGC HFNQGQCLER DGDLTCHIKT TGDNASFFVV GPAVQKQSKY NYAVSYGAWT DRMMEI GMI AIALDEQGSS GSVKTERPKR VGHSMAVSTW ETIKLPEKGN SEGYETSQRQ DSKTPPT AS GGSDTLDVEE GGLPLPVEEE IPDFVGDNPW SDLSTKNSQE EEAMSSESGL RPQLKPPG L PKPQPIRTIR NFDPTPDLVE AWRPDVNPGY SKADVAAATI IAGGSIKDGR SMIDKRNKA VLDGRKSWGS SLASSLTGGT LKASAKSEKL AKLTTSERAR YERIKRQQGS TRASEFLESL LAGEDPDSR F

UniProtKB: Readthrough protein P3-RTD

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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

Concentration1.32 mg/mL
BufferpH: 6 / Component - Concentration: 0.1 mol / L / Component - Name: citrate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 17316
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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