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- EMDB-3785: Structure of Watermelon mosaic virus potyvirus. -

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Basic information

Entry
Database: EMDB / ID: EMD-3785
TitleStructure of Watermelon mosaic virus potyvirus.
Map dataCryoelectron microscopy map of Watermelon mosaic virus filament. Resulting map from Relion postprocessing.
Sample
  • Virus: Watermelon mosaic virus
    • Protein or peptide: coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Keywordsfilamentous virus / potyvirus / plant pathogen / virus
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein
Function and homology information
Biological speciesWatermelon mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZamora M / Mendez-Lopez E
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-66326-P Spain
CitationJournal: Sci Adv / Year: 2017
Title: Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses.
Authors: Miguel Zamora / Eduardo Méndez-López / Xabier Agirrezabala / Rebeca Cuesta / José L Lavín / M Amelia Sánchez-Pina / Miguel A Aranda / Mikel Valle /
Abstract: Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. ...Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å. The atomic model shows a conserved fold for the CPs of flexible filamentous plant viruses, including a universally conserved RNA binding pocket, which is a potential target for antiviral compounds. This conserved fold of the CP is widely distributed in eukaryotic viruses and is also shared by nucleoproteins of enveloped viruses with segmented (-)ssRNA (negative-sense ssRNA) genomes, including influenza viruses.
History
DepositionJul 6, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseSep 27, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5odv
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5odv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3785.png

Downloads & links

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Map

FileDownload / File: emd_3785.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoelectron microscopy map of Watermelon mosaic virus filament. Resulting map from Relion postprocessing.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 230 pix.
= 253. Å		1.1 Å/pix.
x 230 pix.
= 253. Å		1.1 Å/pix.
x 230 pix.
= 253. 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: 0.021 / Movie #1: 0.021
Minimum - Maximum-0.08127693 - 0.11371594
Average (Standard dev.)0.0023535916 (±0.008607002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 253.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z253.000253.000253.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.0810.1140.002

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Supplemental data

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Additional map: Cryoelectron microscopy map of Watermelon mosaic virus filament....

Fileemd_3785_additional.map
AnnotationCryoelectron microscopy map of Watermelon mosaic virus filament. Map generated by applying helical symmetry parameters to Relion postprocessing resulting map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half 1 map of Watermelon mosaic virus...

Fileemd_3785_half_map_1.map
AnnotationUnfiltered half 1 map of Watermelon mosaic virus filament resulting from Relion 3D Refine.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half 2 map of Watermelon mosaic virus...

Fileemd_3785_half_map_2.map
AnnotationUnfiltered half 2 map of Watermelon mosaic virus filament resulting from Relion 3D Refine.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Watermelon mosaic virus

EntireName: Watermelon mosaic virus
Components
  • Virus: Watermelon mosaic virus
    • Protein or peptide: coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Watermelon mosaic virus

SupramoleculeName: Watermelon mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 146500 / Sci species name: Watermelon mosaic virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: coat protein

MacromoleculeName: coat protein / type: protein_or_peptide / ID: 1
Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of ...Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of being high flexible regions in the protein.
Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Watermelon mosaic virus
Molecular weightTheoretical: 31.463412 KDa
SequenceString: SGKEAVENLD AGKESKKDTS GKGDKPQNSQ TGQGSKEQTK TGTVSKDVNV GSKGKEVPRL QKITKKMNLP TVGGKIILSL DHLLEYKPN QVDLFNTRAT KTQFESWYSA VKVEYDLNDE QMGVIMNGFM VWCIDNGTSP DVNGVWVMMD GEEQVEYPLK P IVENAKPT ...String:
SGKEAVENLD AGKESKKDTS GKGDKPQNSQ TGQGSKEQTK TGTVSKDVNV GSKGKEVPRL QKITKKMNLP TVGGKIILSL DHLLEYKPN QVDLFNTRAT KTQFESWYSA VKVEYDLNDE QMGVIMNGFM VWCIDNGTSP DVNGVWVMMD GEEQVEYPLK P IVENAKPT LRQIMHHFSD AAEAYIEMRN SESPYMPRYG LLRNLRDREL ARYAFDFYEV TSKTPNRARE AIAQMKAAAL AG INSRLFG LDGNISTNSE NTERHTARDV NQNMHTLLGM GPPQ

UniProtKB: Genome polyprotein

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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 / Number of copies: 24
Source (natural)Organism: Watermelon 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 2-27 / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.99 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.87 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.3) / Number images used: 50045
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0.3)
FSC plot (resolution estimation)

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