5G52

Crystallographic structure of full particle of Deformed Wing Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.285 

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Literature

Structure of deformed wing virus, a major honey bee pathogen.

Skubnik, K.Novacek, J.Fuzik, T.Pridal, A.Paxton, R.J.Plevka, P.

(2017) Proc Natl Acad Sci U S A 114: 3210-3215

  • DOI: https://doi.org/10.1073/pnas.1615695114
  • Primary Citation of Related Structures:  
    5G51, 5G52, 5L7Q, 5L8Q, 5MUP, 5MV5, 5MV6

  • PubMed Abstract: 

    The worldwide population of western honey bees ( Apis mellifera ) is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) from the family Iflaviridae , together with its vector, the mite Varroa destructor , is likely the major threat to the world's honey bees. However, lack of knowledge of the atomic structures of iflaviruses has hindered the development of effective treatments against them. Here, we present the virion structures of DWV determined to a resolution of 3.1 Å using cryo-electron microscopy and 3.8 Å by X-ray crystallography. The C-terminal extension of capsid protein VP3 folds into a globular protruding (P) domain, exposed on the virion surface. The P domain contains an Asp-His-Ser catalytic triad that is, together with five residues that are spatially close, conserved among iflaviruses. These residues may participate in receptor binding or provide the protease, lipase, or esterase activity required for entry of the virus into a host cell. Furthermore, nucleotides of the DWV RNA genome interact with VP3 subunits. The capsid protein residues involved in the RNA binding are conserved among honey bee iflaviruses, suggesting a putative role of the genome in stabilizing the virion or facilitating capsid assembly. Identifying the RNA-binding and putative catalytic sites within the DWV virion structure enables future analyses of how DWV and other iflaviruses infect insect cells and also opens up possibilities for the development of antiviral treatments.


  • Organizational Affiliation

    Structural Virology, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1243Deformed wing virusMutation(s): 0 
UniProt
Find proteins for Q8B3M2 (Deformed wing virus)
Explore Q8B3M2 
Go to UniProtKB:  Q8B3M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8B3M2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP2250Deformed wing virusMutation(s): 0 
UniProt
Find proteins for Q8B3M2 (Deformed wing virus)
Explore Q8B3M2 
Go to UniProtKB:  Q8B3M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8B3M2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP3397Deformed wing virusMutation(s): 0 
UniProt
Find proteins for Q8B3M2 (Deformed wing virus)
Explore Q8B3M2 
Go to UniProtKB:  Q8B3M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8B3M2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download Ideal Coordinates CCD File 
D [auth C]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.285 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 360.131α = 90
b = 360.131β = 90
c = 360.131γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other