5ND1

Viral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses.

Mata, C.P.Luque, D.Gomez-Blanco, J.Rodriguez, J.M.Gonzalez, J.M.Suzuki, N.Ghabrial, S.A.Carrascosa, J.L.Trus, B.L.Caston, J.R.

(2017) PLoS Pathog 13: e1006755-e1006755

  • DOI: https://doi.org/10.1371/journal.ppat.1006755
  • Primary Citation of Related Structures:  
    5ND1

  • PubMed Abstract: 

    Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues. Despite a lack of sequence similarity between the two proteins, they have a similar α-helical domain, the structural signature shared with the lineage of the dsRNA bluetongue virus-like viruses. Domain insertions in P2 and P4 preferential sites provide additional functions at the capsid outer surface, probably related to enzyme activity. The P2 insertion has a fold similar to that of gelsolin and profilin, two actin-binding proteins with a function in cytoskeleton metabolism, whereas the P4 insertion suggests protease activity involved in cleavage of the P2 383-residue C-terminal region, absent in the mature viral particle. Our results indicate that the intimate virus-fungus partnership has altered the capsid genome-protective and/or receptor-binding functions. Fungal virus evolution has tended to allocate enzyme activities to the virus capsid outer surface.


  • Organizational Affiliation

    Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus Cantoblanco, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein1,357Rosellinia necatrix quadrivirus 1Mutation(s): 0 
UniProt
Find proteins for M1VMJ0 (Rosellinia necatrix quadrivirus 1)
Explore M1VMJ0 
Go to UniProtKB:  M1VMJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1VMJ0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein1,059Rosellinia necatrix quadrivirus 1Mutation(s): 0 
UniProt
Find proteins for M1VHN2 (Rosellinia necatrix quadrivirus 1)
Explore M1VHN2 
Go to UniProtKB:  M1VHN2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1VHN2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTCoot
MODEL REFINEMENTREFMAC5

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-55475-R
Comunidad Autonoma de MadridSpainS2013/MIT-2807

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references
  • Version 1.5: 2024-06-05
    Changes: Advisory, Derived calculations
  • Version 1.6: 2024-06-12
    Changes: Advisory, Derived calculations