1QJZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Work: 0.326 
  • R-Value Observed: 0.326 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1006/jmbi.1999.2787
  • Primary Citation of Related Structures:  
    1QJZ

  • 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 ...

    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.


    Related Citations: 
    • Identification of a Discrete Intermediate in the Assembly/Disassembly of Physalis Mottle Tymovirus Through Mutational Analysis
      Sastri, M., Reddy, S., Krishna, S.S., Murthy, M.R.N., Savithri, H.S.
      (1999) J Mol Biol 289: 905
    • Assembly of Physalis Mottle Virus Capsid Protein in Escherichia Coli and the Role of Amino and Carboxy Termini in the Formation of the Icosahedral Particles
      Sastri, M., Kekuda, R., Gopinath, K., Kumar, C.T.R., Jagath, J.R., Savithri, H.S.
      (1997) J Mol Biol 272: 541
    • Architecture of Physalis Mottle Tymovirus as Probed by Monoclonal Antibodies and Cross-Linking Studies
      Kekuda, R., Karande, A.A., Jacob, A.N.K., Savithri, H.S.
      (1993) Virology 193: 959
    • Structure of Belladonna Mottle Virus: Cross Rotation Function Studies with Southern Bean Mosaic Virus
      Hiremath, C.N., Munshi, S.K., Murthy, M.R.N.
      (1990) Acta Crystallogr B 46: 562
    • Primary Structure of Belladonna Mottle Virus Coat Protein
      Suryanarayana, S., Rao, N.A., Murthy, M.R.N., Savithri, H.S.
      (1989) J Biol Chem 264: 6273
    • Stability of Belladonna Mottle Virus Particles: The Role of Polyamines and Calcium
      Savithri, H.S., Munshi, S.K., Suryanarayana, S., Divakar, S., Murthy, M.R.N.
      (1987) J Gen Virol 68: 1533
    • Symmetry of Belladonna Mottle Virus: Rotation Function Studies
      Munshi, S.K., Hiremath, C.N., Murthy, M.R.N., Savithri, H.S.
      (1987) Acta Crystallogr B 43: 376

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COAT PROTEIN ABC188Physalis mottle virusMutation(s): 0 
Find proteins for P36351 (Physalis mottle virus)
Explore P36351 
Go to UniProtKB:  P36351
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



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