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- PDB-8qkp: Asymmetric structure of Satellite Tobacco Necrosis Virus-Like Par... -

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Basic information

Entry
Database: PDB / ID: 8qkp
TitleAsymmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS2/3 gRNA
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / STNV / CryoEM
Function / homology
Function and homology information


viral capsid / structural molecule activity / metal ion binding / RNA 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
CYTIDINE-5'-MONOPHOSPHATE / GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE -5'-THIO-MONOPHOSPHATE / URIDINE-5'-PHOSPHOROTHIOATE / Capsid protein
Similarity search - Component
Biological speciesSatellite tobacco necrosis virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.26 Å
AuthorsJaved, A. / Mata, P.C. / Stockley, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110145/Z/15/Z United Kingdom
CitationJournal: J Mol Biol / Year: 2024
Title: Visualizing Viral RNA Packaging Signals in Action.
Authors: Emma Wroblewski / Nikesh Patel / Abid Javed / Carlos P Mata / Rebecca Chandler-Bostock / B G Lekshmi / Sabine M Ulamec / Sam Clark / Simon E V Phillips / Neil A Ranson / Reidun Twarock / Peter G Stockley /
Abstract: Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5' two-thirds of the gRNA of Satellite Tobacco Necrosis ...Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5' two-thirds of the gRNA of Satellite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate formation of its T = 1 virus-like particle (VLP). These contacts explain why natural virions only package their positive-sense genomes. Asymmetric cryo-EM reconstructions of these VLPs suggest that interactions occur between amino acid residues in the N-terminal ends of the CP subunits and the gRNA PS loop sequences. The base-paired stems of PSs also act non-sequence-specifically by electrostatically promoting the assembly of CP trimers. Importantly, alterations in PS-CP affinity result in an asymmetric distribution of bound PSs inside VLPs, with fuller occupation of the higher affinity 5' PS RNAs around one vertex, decreasing to an RNA-free opposite vertex within the VLP shell. This distribution suggests that gRNA folding regulates cytoplasmic genome extrusion so that the weakly bound 3' end of the gRNA, containing the RNA polymerase binding site, extrudes first. This probably occurs after cation-loss induced swelling of the CP-shell, weakening contacts between CP subunits. These data reveal for the first time in any virus how differential PS folding propensity and CP affinities support the multiple roles genomes play in virion assembly and infection. The high degree of conservation between the CP fold of STNV-1 and those of the CPs of many other viruses suggests that these aspects of genome function will be widely shared.
History
DepositionSep 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: Capsid protein
P: Capsid protein
Q: Capsid protein
R: Capsid protein
S: Capsid protein
T: Capsid protein
U: Capsid protein
V: Capsid protein
W: Capsid protein
X: Capsid protein
Y: Capsid protein
Z: Capsid protein
a: Capsid protein
b: Capsid protein
c: Capsid protein
d: Capsid protein
e: Capsid protein
f: Capsid protein
g: Capsid protein
h: Capsid protein
i: Capsid protein
j: Capsid protein
k: Capsid protein
l: Capsid protein
m: Capsid protein
n: Capsid protein
o: Capsid protein
p: Capsid protein
q: Capsid protein
r: Capsid protein
s: Capsid protein
t: Capsid protein
u: Capsid protein
v: Capsid protein
w: Capsid protein
x: Capsid protein
y: Capsid protein
z: Capsid protein
0: Capsid protein
1: Capsid protein
2: Capsid protein
3: Capsid protein
4: Capsid protein
5: Capsid protein
6: Capsid protein
7: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,295,736284
Polymers1,245,99260
Non-polymers49,744224
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 60 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#1: Protein ...
Capsid protein


Mass: 20766.531 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Satellite tobacco necrosis virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03606

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Non-polymers , 5 types, 224 molecules

#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 92 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SRA / ADENOSINE -5'-THIO-MONOPHOSPHATE


Type: RNA linking / Mass: 363.287 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C10H14N5O6PS
#4: Chemical...
ChemComp-SSU / URIDINE-5'-PHOSPHOROTHIOATE / SP-SULFUR-SUBSTITUTED URIDINE


Type: RNA linking / Mass: 340.247 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C9H13N2O8PS
#5: Chemical...
ChemComp-G / GUANOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 363.221 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C10H14N5O8P
#6: Chemical...
ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C9H14N3O8P

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Satellite tobacco necrosis virus 1 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Satellite tobacco necrosis virus 1
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Nicotiana tabacum
Virus shellDiameter: 180 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHepes1
23 mMCalcium ChlorideCaCl21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified STNV-1 VLP with PS 2/3 genomic RNA.
Specimen supportGrid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3750 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 47.6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9979
Image scansMovie frames/image: 39

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION3particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera8.6model fittingRigid-body fit
9cryoSPARC4.2initial Euler assignment
10cryoSPARC4.2final Euler assignment
11RELION3classification
12cryoSPARC4.23D reconstruction
13PHENIX1.9model refinement
14Coot0.9.6model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 509873
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81619 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 265.1 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 4bcu

4bcu


Accession code: 4bcu / Source name: PDB / Type: experimental model

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