Ryegrass mottle virus protease domain

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

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This is version 1.2 of the entry. See complete history


VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure.

Kalnins, G.Ludviga, R.Kalnciema, I.Resevica, G.Zeltina, V.Bogans, J.Tars, K.Zeltins, A.Balke, I.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24065347
  • Primary Citation of Related Structures:  
    6FEZ, 6FF0, 7YZV

  • PubMed Abstract: 

    Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro-VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro-VPg complex during interaction is lacking. Here, we solved a full Pro-VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans , VPg can also mediate Pro in free form. Additionally, we observed Ca 2+ and Zn 2+ inhibitory effects on the Pro cleavage activity.

  • Organizational Affiliation

    Structural Biology Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease domain
A, B
199Ryegrass mottle virusMutation(s): 0 
Find proteins for A0MCW0 (Ryegrass mottle virus)
Explore A0MCW0 
Go to UniProtKB:  A0MCW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0MCW0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.11α = 90
b = 115.99β = 105.27
c = 57.92γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2019-04-17 
  • Deposition Author(s): Kalnins, G.

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description