7YZV | pdb_00007yzv

Ryegrass mottle virus serine protease domain S159A mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.263 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 20.87 kDa 
  • Atom Count: 1,452 
  • Modeled Residue Count: 185 
  • Deposited Residue Count: 199 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase199Ryegrass mottle virusMutation(s): 1 
EC: 2.7.7.48
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.263 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.222α = 90
b = 36.95β = 126.291
c = 69.498γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2022-03-02 
    • Deposition Author(s): Kalnins, G.
Funding OrganizationLocationGrant Number
European Regional Development FundEuropean Union1.1.1.2/VIAA/3/19/462

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary