Three Dimensional Structure of Physalis Mottle Virus : Implications for the Viral Assembly

Experimental Data Snapshot

  • Resolution: 3.80 Å
  • R-Value Work: 0.326 
  • R-Value Observed: 0.326 

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Three Dimensional Structure of Physalis Movirus: Implications for the Viral Assembly

Krishna, S.S.Hiremath, C.N.Munshi, S.K.Prahadeeswaran, D.Sastri, M.Savithri, H.S.Murthy, M.R.N.

(1999) J Mol Biol 289: 919

  • DOI: https://doi.org/10.1006/jmbi.1999.2787
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure of the T=3 single stranded RNA tymovirus, physalis mottle virus (PhMV), has been determined to 3.8 A resolution. PhMV crystals belong to the rhombohedral space group R 3, with one icosahedral particle in the unit cell leading to 20-fold non-crystallographic redundancy. Polyalanine coordinates of the related turnip yellow mosaic virus (TYMV) with which PhMV coat protein shares 32 % amino acid sequence identity were used for obtaining the initial phases. Extensive phase refinement by real space molecular replacement density averaging resulted in an electron density map that revealed density for most of the side-chains and for the 17 residues ordered in PhMV, but not seen in TYMV, at the N terminus of the A subunits. The core secondary and tertiary structures of the subunits have a topology consistent with the capsid proteins of other T=3 plant viruses. The N-terminal arms of the A subunits, which constitute 12 pentamers at the icosahedral 5-fold axes, have a conformation very different from the conformations observed in B and C subunits that constitute hexameric capsomers with near 6-fold symmetry at the icosahedral 3-fold axes. An analysis of the interfacial contacts between protein subunits indicates that the hexamers are held more strongly than pentamers and hexamer-hexamer contacts are more extensive than pentamer-hexamer contacts. These observations suggest a plausible mechanism for the formation of empty capsids, which might be initiated by a change in the conformation of the N-terminal arm of the A subunits. The structure also provides insights into immunological and mutagenesis results. Comparison of PhMV with the sobemovirus, sesbania mosaic virus reveals striking similarities in the overall tertiary fold of the coat protein although the capsid morphologies of these two viruses are very different.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science Bangalore, 560 012, India. mrn@mbu.iisc.ernet.in

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
188Physalis mottle virusMutation(s): 0 
Find proteins for P36351 (Physalis mottle virus)
Explore P36351 
Go to UniProtKB:  P36351
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36351
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.80 Å
  • R-Value Work: 0.326 
  • R-Value Observed: 0.326 
  • Space Group: R 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 294.65α = 59.91
b = 294.65β = 59.91
c = 294.65γ = 59.91
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-30
    Changes: Data collection, Structure summary
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description