1E57

PHYSALIS MOTTLE VIRUS: EMPTY CAPSID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Studies on the Empty Capsids of Physalis Mottle Virus

Krishna, S.S.Sastri, M.Savithri, H.S.Murthy, M.R.N.

(2001) J Mol Biol 307: 1035

  • DOI: 10.1006/jmbi.2001.4533
  • Primary Citation of Related Structures:  
    1E57

  • PubMed Abstract: 
  • The three-dimensional crystal structure of the empty capsid of Physalis mottle tymovirus has been determined to 3.2 A resolution. The empty capsids crystallized in the space group P1, leading to 60-fold non-crystallographic redundancy. The known structure of Physalis mottle virus was used as a phasing model to initiate the structure determination by real-space electron-density averaging ...

    The three-dimensional crystal structure of the empty capsid of Physalis mottle tymovirus has been determined to 3.2 A resolution. The empty capsids crystallized in the space group P1, leading to 60-fold non-crystallographic redundancy. The known structure of Physalis mottle virus was used as a phasing model to initiate the structure determination by real-space electron-density averaging. The main differences between the structures of the native and the empty capsids were in residues 10 to 28 of the A-subunit, residues 1 to 9 of the B-subunit and residues 1 to 5 of the C-subunit, which are ordered only in the native virus particles. An analysis of the subunit disposition reveals that the virus has expanded radially outward by approximately 1.8 A in the empty particles. The A-subunits move in a direction that makes 10 degrees to the icosahedral 5-fold axes of symmetry. The B and C-subunits move along vectors making 12 degrees and 15 degrees to the quasi 6-fold axes. The quaternary organization of the pentameric and hexameric capsomeres are not altered significantly. However, the pentamer-hexamer contacts are reduced. Therefore, encapsidation of RNA appears to cause a reduction in the particle radius concomittant with the ordering of the N-terminal arm in the three subunits. These structural changes in Physalis mottle virus appear to be larger than the corresponding changes observed in viruses for which both the empty and full particle structures have been determined.


    Related Citations: 
    • 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
    • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHYSALIS MOTTLE VIRUSA, B, C188Physalis 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: 3.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 289.64α = 63.59
b = 287.722β = 61.39
c = 295.226γ = 62.94
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
MARSCALEdata scaling
GLRFphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-26
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Version format compliance