3ES5 | pdb_00003es5

Crystal Structure of Partitivirus (PsV-F)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.267 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.238 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3ES5

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 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.

Macromolecule Content 

  • Total Structure Weight: 93.18 kDa 
  • Atom Count: 5,919 
  • Modeled Residue Count: 757 
  • Deposited Residue Count: 840 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.267 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.238 (DCC) 
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

View Full Validation Report



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