3ES5

Crystal Structure of Partitivirus (PsV-F)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Atomic structure reveals the unique capsid organization of a dsRNA virus.

Pan, J.Dong, L.Lin, L.Ochoa, W.F.Sinkovits, R.S.Havens, W.M.Nibert, M.L.Baker, T.S.Ghabrial, S.A.Tao, Y.J.

(2009) Proc Natl Acad Sci U S A 106: 4225-4230

  • DOI: https://doi.org/10.1073/pnas.0812071106
  • Primary Citation of Related Structures:  
    3ES5

  • PubMed Abstract: 

    For most dsRNA viruses, the genome-enclosing capsid comprises 120 copies of a single capsid protein (CP) organized into 60 icosahedrally equivalent dimers, generally identified as 2 nonsymmetricallyinteracting CP molecules with extensive lateral contacts. The crystal structure of a partitivirus, Penicillium stoloniferum virus F (PsV-F), reveals a different organization, in which the CP dimer is related by almost-perfect local 2-fold symmetry, forms prominent surface arches, and includes extensive structure swapping between the 2 subunits. An electron cryomicroscopy map of PsV-F shows that the disordered N terminus of each CP molecule interacts with the dsRNA genome and probably participates in its packaging or transcription. Intact PsV-F particles mediate semiconservative transcription, and transcripts are likely to exit through negatively charged channels at the icosahedral 5-fold axes. Other findings suggest that the PsV-F capsid is assembled from dimers of CP dimers, with an arrangement similar to flavivirus E glycoproteins.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative capsid protein
A, B
420Penicillium stoloniferum virus FMutation(s): 0 
UniProt
Find proteins for Q4G3H1 (Penicillium stoloniferum virus F)
Explore Q4G3H1 
Go to UniProtKB:  Q4G3H1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4G3H1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.248 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 459.266α = 90
b = 459.266β = 90
c = 459.266γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
RAVEmodel building
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RAVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description