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- EMDB-15346: CryoEM structure of sweet potato mild mottle virus VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-15346
TitleCryoEM structure of sweet potato mild mottle virus VLP
Map dataSharpened map.
Sample
  • Virus: Sweet potato mild mottle virus
    • Protein or peptide: Polyprotein
    • RNA: Single-stranded RNA
KeywordsPlant virus / coat protein / VLP / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


viral capsid / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding
Similarity search - Function
Potyvirus coat protein / Potyvirus coat protein / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesSweet potato mild mottle virus / Nicotiana tabacum (common tobacco)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJaved A / Byrne BM / Ranson N / Lomonosoff G
Funding support Spain, United Kingdom, 4 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-105692RB-100 Spain
Ministerio de Ciencia e Innovacion (MCIN)CEX2019-000902-S Spain
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001669/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004703/1 United Kingdom
CitationJournal: Commun Biol / Year: 2023
Title: CryoEM and stability analysis of virus-like particles of potyvirus and ipomovirus infecting a common host.
Authors: Ornela Chase / Abid Javed / Matthew J Byrne / Eva C Thuenemann / George P Lomonossoff / Neil A Ranson / Juan José López-Moya /
Abstract: Sweet potato feathery mottle virus (SPFMV) and Sweet potato mild mottle virus (SPMMV) are members of the genera Potyvirus and Ipomovirus, family Potyviridae, sharing Ipomoea batatas as common host, ...Sweet potato feathery mottle virus (SPFMV) and Sweet potato mild mottle virus (SPMMV) are members of the genera Potyvirus and Ipomovirus, family Potyviridae, sharing Ipomoea batatas as common host, but transmitted, respectively, by aphids and whiteflies. Virions of family members consist of flexuous rods with multiple copies of a single coat protein (CP) surrounding the RNA genome. Here we report the generation of virus-like particles (VLPs) by transient expression of the CPs of SPFMV and SPMMV in the presence of a replicating RNA in Nicotiana benthamiana. Analysis of the purified VLPs by cryo-electron microscopy, gave structures with resolutions of 2.6 and 3.0 Å, respectively, showing a similar left-handed helical arrangement of 8.8 CP subunits per turn with the C-terminus at the inner surface and a binding pocket for the encapsidated ssRNA. Despite their similar architecture, thermal stability studies reveal that SPMMV VLPs are more stable than those of SPFMV.
History
DepositionJul 5, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15346.png

Downloads & links

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Map

FileDownload / File: emd_15346.map.gz / Format: CCP4 / Size: 34.3 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.)
1.07 Å/pix.
x 208 pix.
= 221.52 Å		1.07 Å/pix.
x 208 pix.
= 221.52 Å		1.07 Å/pix.
x 208 pix.
= 221.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0810315 - 0.14286922
Average (Standard dev.)0.0004678518 (±0.0121175535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 221.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half 1 map.

Fileemd_15346_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_15346_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 : Sweet potato mild mottle virus

EntireName: Sweet potato mild mottle virus
Components
  • Virus: Sweet potato mild mottle virus
    • Protein or peptide: Polyprotein
    • RNA: Single-stranded RNA

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Supramolecule #1: Sweet potato mild mottle virus

SupramoleculeName: Sweet potato mild mottle virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 41459 / Sci species name: Sweet potato mild mottle virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Ipomoea batatas (sweet potato)
Molecular weightTheoretical: 38 kDa/nm
Virus shellShell ID: 1 / Diameter: 130.0 Å

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Macromolecule #1: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sweet potato mild mottle virus
Molecular weightTheoretical: 34.28284 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: ASTSKTIEEL QQEMEDLDAD TTITVVQRET QKARIREQIE TLRAQQMVRP SEAQLQPDVT PTQIVTFEPP RVTGFGALWI PRQQRNYMT TAYIEKIKAY VPHSNLIESG LASEAQLTSW IENTCRDYQV SMDVFMTTVL PAWIVNCIIN GTSQERTNEH T WRAVIMAN ...String:
ASTSKTIEEL QQEMEDLDAD TTITVVQRET QKARIREQIE TLRAQQMVRP SEAQLQPDVT PTQIVTFEPP RVTGFGALWI PRQQRNYMT TAYIEKIKAY VPHSNLIESG LASEAQLTSW IENTCRDYQV SMDVFMTTVL PAWIVNCIIN GTSQERTNEH T WRAVIMAN MEDQEVLYYP IKPIIVNAQP TLRQVMRHFG EQAVAQYMNS LQAGKPFTVK GAVTAGYANV QDAWLGIDFL RD TMQLTTK QMEVKHQIIA ANVTRRKIRV FALAAPGDGD ELDTERHVVD DVARGRHSLR GAQLD

UniProtKB: Polyprotein

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Macromolecule #2: Single-stranded RNA

MacromoleculeName: Single-stranded RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Nicotiana tabacum (common tobacco)
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

Concentration0.5 mg/mL
BufferpH: 7 / Component - Concentration: 50.0 mM / Component - Formula: NaPO4 / Component - Name: Sodium phosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3ul of sample applied to each grid..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2260 / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 3.97 Å
Applied symmetry - Helical parameters - Δ&Phi: 41.29 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 38705
Segment selectionNumber selected: 329573 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: OTHER / Details: Cylinder with the diameter of the helical virus.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 123.7 / Target criteria: Correlation Coefficient
Output model

PDB-8acc:
CryoEM structure of sweet potato mild mottle virus VLP

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