7MIC

Maize rayado fino virus protease in complex with Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The endopeptidase of the maize-affecting Marafivirus type member maize rayado fino virus doubles as a deubiquitinase.

Patel, A.McBride, J.A.M.Mark, B.L.

(2021) J Biol Chem 297: 100957-100957

  • DOI: 10.1016/j.jbc.2021.100957
  • Primary Citation of Related Structures:  
    7MIA, 7MIC

  • PubMed Abstract: 
  • Marafiviruses are capable of persistent infection in a range of plants that have importance to the agriculture and biofuel industries. Although the genomes of a few of these viruses have been studied in-depth, the composition and processing of the polyproteins produced from their main open reading frames have not ...

    Marafiviruses are capable of persistent infection in a range of plants that have importance to the agriculture and biofuel industries. Although the genomes of a few of these viruses have been studied in-depth, the composition and processing of the polyproteins produced from their main open reading frames have not. The marafivirus polyprotein consists of essential proteins that form the viral replicase, as well as structural proteins for virus assembly. It has been proposed that marafiviruses code for cysteine proteases within their polyproteins, which act as endopeptidases to autocatalytically cleave the polyprotein into functional domains. Further, it has also been suggested that marafivirus endopeptidases may have deubiquitinating activity, which has been shown to enhance viral replication by downregulating viral protein degradation by the ubiquitin proteasomal pathway as well as tampering with cell signaling associated with innate antiviral responses in other +ssRNA viruses. Here we provide the first evidence of cysteine proteases from six different marafiviruses that harbour deubiquitinating activity and reveal intra-genus differences towards ubiquitin linkage types. We also examine the structural basis of the endopeptidase/deubiquitinase from the marafivirus type member, Maize rayado fino virus. Structures of the enzyme alone and bound to ubiquitin reveal marked structural rearrangements that occur upon binding of Ub and provide insights into substrate specificity and differences that set it apart from other viral cysteine proteases.


    Organizational Affiliation

    Department of Microbiology, University of Manitoba, Winnipeg, Canada, R3T 2N2. Electronic address: brian.mark@umanitoba.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA replication proteinA154Maize rayado fino virusMutation(s): 1 
Gene Names: ORF1
EC: 2.7.7.48 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for Q91TW9 (Maize rayado fino virus (isolate Costa Rica/Guapiles))
Explore Q91TW9 
Go to UniProtKB:  Q91TW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91TW9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB76Homo sapiensMutation(s): 1 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3CN (Subject of Investigation/LOI)
Query on 3CN

Download Ideal Coordinates CCD File 
D [auth B]3-AMINOPROPANE
C3 H9 N
WGYKZJWCGVVSQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.72α = 90
b = 75.72β = 90
c = 79.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-04-16 
  • Released Date: 2021-07-21 
  • Deposition Author(s): Patel, A., Mark, B.L.

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2021-08-11
    Changes: Database references