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- EMDB-4740: Atomic structure of potato virus X, the prototype of the Alphafle... -

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Basic information

Entry
Database: EMDB / ID: EMD-4740
TitleAtomic structure of potato virus X, the prototype of the Alphaflexiviridae family
Map data
Sample
  • Virus: Potato virus X
    • Protein or peptide: Coat protein
    • RNA: polyU RNA
  • Ligand: water
KeywordsVirus / Coat Protein / RNA
Function / homologyPotexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / helical viral capsid / ribonucleoprotein complex / structural molecule activity / Coat protein / Coat protein
Function and homology information
Biological speciesPotato virus X
Methodhelical reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsGrinzato A / Kandiah E
CitationJournal: Nat Chem Biol / Year: 2020
Title: Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family.
Authors: Alessandro Grinzato / Eaazhisai Kandiah / Chiara Lico / Camilla Betti / Selene Baschieri / Giuseppe Zanotti /
Abstract: Potato virus X (PVX) is a positive-sense single-stranded RNA (ssRNA) filamentous plant virus belonging to the Alphaflexiviridae family, considered in recent years as a tool for nanotechnology ...Potato virus X (PVX) is a positive-sense single-stranded RNA (ssRNA) filamentous plant virus belonging to the Alphaflexiviridae family, considered in recent years as a tool for nanotechnology applications. We present the cryo-electron microscopy structure of the PVX particle at a resolution of 2.2 Å. The well-defined density of the coat proteins and of the genomic RNA allowed a detailed analysis of protein-RNA interactions, including those mediated by solvent molecules. The particle is formed by repeated segments made of 8.8 coat proteins, forming a left-handed helical structure. The RNA runs in an internal crevice along the virion, packaged in 5-nucleotide repeats in which the first four bases are stacked in the classical way, while the fifth is rotated and nearly perpendicular. The resolution of the structure described here suggests a mechanism for the virion assembly and potentially provides a platform for the rational design of antiviral compounds and for the use of PVX in nanotechnology.
History
DepositionMar 28, 2019-
Header (metadata) releaseMar 18, 2020-
Map releaseMar 18, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r7g
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6r7g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4740.png

Downloads & links

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Map

FileDownload / File: emd_4740.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.72 Å		0.83 Å/pix.
x 360 pix.
= 297.72 Å		0.83 Å/pix.
x 360 pix.
= 297.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.045
Minimum - Maximum-0.1463817 - 0.26963514
Average (Standard dev.)0.00079593103 (±0.008798706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8270.8270.827
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z297.720297.720297.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1460.2700.001

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Supplemental data

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Sample components

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Entire : Potato virus X

EntireName: Potato virus X
Components
  • Virus: Potato virus X
    • Protein or peptide: Coat protein
    • RNA: polyU RNA
  • Ligand: water

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Supramolecule #1: Potato virus X

SupramoleculeName: Potato virus X / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 12183 / Sci species name: Potato virus X / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Potato virus X
Molecular weightTheoretical: 22.519514 KDa
SequenceString: ASGLFTIPDG DFFSTARAIV ASNAVATNED LSKIEAIWKD MKVPTDTMAQ AAWDLVRHCA DVGSSAQTEM IDTGPYSNGI SRARLAAAI KEVCTLRQFC MKYAPVVWNW MLTNNSPPAN WQAQGFKPEH KFAAFDFFNG VTNPAAIMPK EGLIRPPSEA E MNAAQTAA ...String:
ASGLFTIPDG DFFSTARAIV ASNAVATNED LSKIEAIWKD MKVPTDTMAQ AAWDLVRHCA DVGSSAQTEM IDTGPYSNGI SRARLAAAI KEVCTLRQFC MKYAPVVWNW MLTNNSPPAN WQAQGFKPEH KFAAFDFFNG VTNPAAIMPK EGLIRPPSEA E MNAAQTAA FVKITKARAQ SNDFASLDAA VTRGRITGTT TAEAVVTLPP P

UniProtKB: Coat protein

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Macromolecule #2: polyU RNA

MacromoleculeName: polyU RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Potato virus X
Molecular weightTheoretical: 21.080488 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUU

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 92 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 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: 3.96 Å
Applied symmetry - Helical parameters - Δ&Phi: 40.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 331130
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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