8C6V

The RNA silencing suppressor P8 from High-Plains Wheat Mosaic Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The RNA Silencing Suppressor P8 From High Plains Wheat Mosaic Virus is a Functional Tetramer.

Hamo, S.Izhaki-Tavor, L.S.Tatineni, S.Dessau, M.

(2024) J Mol Biol 436: 168870-168870

  • DOI: https://doi.org/10.1016/j.jmb.2024.168870
  • Primary Citation of Related Structures:  
    8C6V

  • PubMed Abstract: 

    In plants, RNA interference (RNAi) serves as a critical defense mechanism against viral infections by regulating gene expression. However, viruses have developed RNA silencing suppressor (RSS) proteins to evade this defense mechanism. The High Plains wheat mosaic virus (HPWMoV) is responsible for the High Plains disease in wheat and produces P7 and P8 proteins, which act as RNA silencing suppressors. P8, in particular, lacks sequence similarity to known suppressors, prompting inquiries into its structure and function. Here, we present a comprehensive analysis of P8, elucidating its structure and function. Using X-ray crystallography, we resolved the full-length P8 structure at 1.9 Å resolution, revealing a tetrameric arrangement formed by two identical dimers. Through structure-based mutagenesis, biochemical assays, and functional studies in plants, we demonstrate that HPWMoV P8's RNA silencing suppression activity relies on its oligomeric state. Contrary to previous report, our findings indicate that while a P8 fused to maltose-binding protein (MBP-P8) was hypothesized to bind short double-stranded RNA, the native P8 tetramer does not interact with small interfering RNA (siRNA). This suggests an alternative mechanism for its function, yet to be determined. Our study sheds light on the structural and functional characteristics of HPWMoV P8, providing valuable insights into the complex interplay between viral suppressors and host defense mechanisms. SIGNIFICANCE STATEMENT Effective action to address malnutrition in all its forms requires an understanding of the mechanisms affecting it. Wheat, crucial for human and animal consumption, faces threats from biotic and abiotic stresses. RNA silencing is a key defense against viral infections in plants. Plant viruses employ various mechanisms, including encoding viral RNA silencing suppression (VRS) proteins, to evade host immune responses. Despite the conservation of RNA-silencing pathways, viral RSS proteins exhibit diverse sequences, structures, and mechanisms. Our study focuses on P8, an RSS protein from HPWMoV. Understanding its structure and assembly is a crucial step toward comprehending how these viruses counteract host defenses, aiding in combatting malnutrition.


  • Organizational Affiliation

    Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P8 RNA silencing suppressorA,
B [auth C],
C [auth D],
D [auth B]
178Emaravirus triticiMutation(s): 0 
UniProt
Find proteins for A0A076V8I4 (Emaravirus tritici)
Explore A0A076V8I4 
Go to UniProtKB:  A0A076V8I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A076V8I4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
K [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth C],
H [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
F [auth C],
G [auth C],
I [auth D]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.96α = 90
b = 152.39β = 101.01
c = 65.4γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael401/18

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references, Structure summary
  • Version 1.2: 2024-12-11
    Changes: Database references