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- EMDB-18466: Symmetric structure of Satellite Tobacco Necrosis Virus-Like Part... -

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Basic information

Entry
Database: EMDB / ID: EMD-18466
TitleSymmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA
Map dataSharpened map
Sample
  • Virus: Satellite tobacco necrosis virus 1
    • Protein or peptide: Capsid protein
  • Ligand: CALCIUM ION
KeywordsSTNV / CryoEM / 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: 2.39 Å
AuthorsJaved A / Mata PC / Stockley P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust110145/Z/15/Z United Kingdom
CitationJournal: To Be Published
Title: Virion assembly is regulated by sequence-specific and flexible genomic RNA-coat protein contacts
Authors: Wroblewski E / Javed A / Mata PC / Patel N / Leonov G / Philips VES / Twarock R / Stockley GP
History
DepositionSep 15, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18466.png

Downloads & links

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Map

FileDownload / File: emd_18466.map.gz / Format: CCP4 / Size: 61 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 252 pix.
= 268.38 Å		1.07 Å/pix.
x 252 pix.
= 268.38 Å		1.07 Å/pix.
x 252 pix.
= 268.38 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: 0.03
Minimum - Maximum-0.122058965 - 0.29079837
Average (Standard dev.)0.0012173123 (±0.018406468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-126-126-126
Dimensions252252252
Spacing252252252
CellA=B=C: 268.38 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_18466_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 map 1

Fileemd_18466_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_18466_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: CALCIUM 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 / NCBI-ID: 12445 / Sci species name: Satellite tobacco necrosis virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Nicotiana tabacum (common tobacco)
Virus shellShell ID: 1 / Diameter: 180.0 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: 60 / Enantiomer: LEVO
Source (natural)Organism: Satellite tobacco necrosis virus 1
Molecular weightTheoretical: 20.766531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RKSATMRAVK RMINTHLEHK RFALINSGNT NATAGTVQNL SNGIIQGDDI NQRSGDQVRI VSHKLHVRGT AITVSQTFRF IWFRDNMNR GTTPTVLEVL NTANFMSQYN PITLQQKRFT ILKDVTLNCS LTGESIKDRI INLPGQLVNY NGATAVAASN G PGAIFMLQ IGDSLVGLWD SSYEAVYTDA

UniProtKB: Capsid protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 92 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMHepes
3.0 mMCalcium ChlorideCaCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified STNV VLP with PS 1-5 gRNA

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 11550 / Average electron dose: 49.5 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: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 178000
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

Particle selectionNumber selected: 502684
Startup modelType of model: INSILICO MODEL / In silico model: Ab-intio C1 map generated from dataset.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 78988
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final 3D classificationNumber classes: 5 / Avg.num./class: 40000 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4bcu


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 129.1 / Target criteria: Cross-correlation coefficient
Output model

PDB-8qkm:
Symmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA

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