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- EMDB-53395: Satellite Tobacco Necrosis Virus-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-53395
TitleSatellite Tobacco Necrosis Virus-1
Map dataSharpened map at 2.77 A resolution used for model building and refinement
Sample
  • Virus: Satellite tobacco necrosis virus 1
    • Protein or peptide: Capsid protein
  • Ligand: MAGNESIUM ION
KeywordsssRNA plant virus / icosahedral / RNA packaging / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


viral capsid / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Satellite tobacco necrosis virus coat protein-like / Satellite tobacco necrosis virus coat protein / Satellite virus coat / Satellite virus coat domain superfamily / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesSatellite tobacco necrosis virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsSaunders K / Shah S / Peyret H / Meshcheriakova Y / Richardson J / Eltschkner S / Lawson DM / Lomonossoff G
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y005732/1 United Kingdom
CitationJournal: J Mol Biol / Year: 2025
Title: The Specificity of RNA Packaging in Isometric RNA Plant Viruses is Principally Determined by Replication.
Authors: Keith Saunders / Sachin N Shah / Hadrien Peyret / Yulia Meshcheriakova / Jake Richardson / Sandra Eltschkner / David M Lawson / George P Lomonossoff /
Abstract: A potato virus X (PVX)-based transient expression system (pEff) that produces replicating RNA has been used to examine the specificity of RNA packaging in the isometric viruses, turnip crinkle virus ...A potato virus X (PVX)-based transient expression system (pEff) that produces replicating RNA has been used to examine the specificity of RNA packaging in the isometric viruses, turnip crinkle virus (TCV) and satellite tobacco necrosis virus-1 (STNV-1). Expression of the coat proteins from the subgenomic RNA derived from the replicating PVX genome results in the efficient production of virus-like particles (VLPs), indistinguishable in structure from native virus particles, and encapsidation of both the subgenomic RNA and truncated versions of the replicating genomic RNA. Non-specific encapsidation of host RNA (which is not replicating) could not be detected in this system, implying that replication is the major determinant of packaging in isometric as well as filamentous positive-strand RNA plant viruses. We further utilised the system to investigate the role of putative packaging signals previously identified within the coat protein open reading frames of both TCV and STNV-1. The results show that eliminating the hairpin structures previously identified as packaging signals has no detectable effect on the specificity of RNA packaging. Replacement of the 213 nucleotide sequence within the TCV coat protein coding region, believed to be important for genomic packaging, with an equivalent sequence codon-optimised for Plasmodium falciparum resulted in less efficient capsid formation and RNA packaging, but did not alter packaging specificity; addition of copies of the wild-type sequence did not complement the defects. We propose that replication is the major determinant of genome packaging specificity in plant RNA viruses, while packaging signals may play a role in packaging efficiency.
History
DepositionApr 11, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53395.png

Downloads & links

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Map

FileDownload / File: emd_53395.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map at 2.77 A resolution used for model building and refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 500 pix.
= 470. Å		0.94 Å/pix.
x 500 pix.
= 470. Å		0.94 Å/pix.
x 500 pix.
= 470. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.75441986 - 1.3217201
Average (Standard dev.)-0.00062968663 (±0.043324903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 470.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53395_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_53395_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_53395_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_53395_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Satellite tobacco necrosis virus 1

EntireName: Satellite tobacco necrosis virus 1
Components
  • Virus: Satellite tobacco necrosis virus 1
    • Protein or peptide: Capsid protein
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Satellite tobacco necrosis virus 1

SupramoleculeName: Satellite tobacco necrosis virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: The complete STNV coat protein gene was inserted into the pEff vector. Expression was initiated by infiltrating leaves of Nicotiana benthamiana with suspensions of Agrobacterium tumefaciens ...Details: The complete STNV coat protein gene was inserted into the pEff vector. Expression was initiated by infiltrating leaves of Nicotiana benthamiana with suspensions of Agrobacterium tumefaciens strain LBA4404 harbouring this vector.
NCBI-ID: 12445 / Sci species name: Satellite tobacco necrosis virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 1.30 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 200.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Satellite tobacco necrosis virus 1
Molecular weightTheoretical: 21.739645 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MAKQQNNRRK SATMRAVKRM INTHLEHKRF ALINSGNTNA TAGTVQNLSN GIIQGDDINQ RSGDQVRIVS HKLHVRGTAI TVSQTFRFI WFRDNMNRGT TPTVLEVLNT ANFMSQYNPI TLQQKRFTIL KDVTLNCSLT GESIKDRIIN LPGQLVNYNG A TAVAASNG ...String:
MAKQQNNRRK SATMRAVKRM INTHLEHKRF ALINSGNTNA TAGTVQNLSN GIIQGDDINQ RSGDQVRIVS HKLHVRGTAI TVSQTFRFI WFRDNMNRGT TPTVLEVLNT ANFMSQYNPI TLQQKRFTIL KDVTLNCSLT GESIKDRIIN LPGQLVNYNG A TAVAASNG PGAIFMLQIG DSLVGLWDSS YEAVYTDA

UniProtKB: Capsid protein

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration2.92 mg/mL
BufferpH: 7.4 / Details: 1 x phosphate-buffered saline
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
Details: glow discharged for 60 seconds at 8 mA using an ACE 200 (Leica Microsystems)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS F200C
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: TFS FALCON 4i (4k x 4k) / #0 - Digitization - Dimensions - Width: 4096 pixel / #0 - Digitization - Dimensions - Height: 4096 pixel / #0 - Number grids imaged: 1 / #0 - Number real images: 2703 / #0 - Average exposure time: 2.85 sec. / #0 - Average electron dose: 30.0 e/Å2
#0 - Details: The particles were densely packed showing mostly 5-fold views
#1 - Image recording ID: 2 / #1 - Film or detector model: TFS FALCON 4i (4k x 4k) / #1 - Digitization - Dimensions - Width: 4096 pixel / #1 - Digitization - Dimensions - Height: 4096 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 575 / #1 - Average exposure time: 2.82 sec. / #1 - Average electron dose: 30.0 e/Å2
#1 - Details: Regions with a lower particle density were selected, giving additional views, but still dominated by 5-folds.
#2 - Image recording ID: 3 / #2 - Film or detector model: TFS FALCON 4i (4k x 4k) / #2 - Digitization - Dimensions - Width: 4096 pixel / #2 - Digitization - Dimensions - Height: 4096 pixel / #2 - Number grids imaged: 1 / #2 - Number real images: 985 / #2 - Average exposure time: 3.49 sec. / #2 - Average electron dose: 40.0 e/Å2
#2 - Details: Data were collected with a positive 20 degree tilt giving a better distribution of views.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 2394377 / Details: combined figure from the 3 datasets
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2buk

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 207142
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2buk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 43 / Target criteria: cross-correlation coefficient
Output model

PDB-9qve:
Satellite Tobacco Necrosis Virus-1

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