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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: To Be Published
Title: The specificity of RNA packaging in isometric RNA plant viruses is principally determined by replication
Authors: Saunders K / Shah S / Peyret H / Meshcheriakova Y / Richardson J / Eltschkner S / Lawson DM / Lomonossoff G
History
DepositionApr 11, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 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

Projections

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

Projections

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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