Sesbania mosaic virus capsid protein dimer mutant (rCP-DEL-N65-W170K)

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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This is version 1.6 of the entry. See complete history


A Single Point Mutation Disrupts the Capsid Assembly in Sesbania Mosaic Virus Resulting in a Stable Isolated Dimer.

Pappachan, A.Chinnathambi, S.Satheshkumar, P.S.Savithri, H.S.Murthy, M.R.N.

(2009) Virology 392: 215

  • DOI: https://doi.org/10.1016/j.virol.2009.06.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Protein-protein interactions play a crucial role in virus assembly and stability. With the view of disrupting capsid assembly and capturing smaller oligomers, interfacial residue mutations were carried out in the coat protein gene of Sesbania Mosaic Virus, a T=3 ss (+) RNA plant virus. A single point mutation of a Trp 170 present at the five-fold interface of the virus to a charged residue (Glu or Lys) arrested assembly of virus like particles and resulted in stable soluble dimers of the capsid protein. The X-ray crystal structure of one of the isolated dimer mutants - rCPDeltaN65W170K was determined to a resolution of 2.65 A. Detailed analysis of the dimeric mutant protein structure revealed that a number of structural changes take place, especially in the loop and interfacial regions during the course of assembly. The isolated dimer was "more relaxed" than the dimer found in the T=3 or T=1 capsids. The isolated dimer does not bind Ca(2+) ion and consequently four C-terminal residues are disordered. The FG loop, which interacts with RNA in the virus, has different conformations in the isolated dimer and the intact virus suggesting its flexible nature and the conformational changes that accompany assembly. The isolated dimer mutant was much less stable when compared to the assembled capsids, suggesting the importance of inter-subunit interactions and Ca(2+) mediated interactions in the stability of the capsids. With this study, SeMV becomes the first icosahedral virus for which X-ray crystal structures of T=3, T=1 capsids as well as a smaller oligomer of the capsid protein have been determined.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
203Sesbania mosaic virusMutation(s): 1 
Find proteins for Q9EB06 (Sesbania mosaic virus)
Explore Q9EB06 
Go to UniProtKB:  Q9EB06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EB06
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.88α = 81.07
b = 41.95β = 75
c = 68.65γ = 84.25
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-04-17
    Changes: Database references
  • Version 1.3: 2015-02-25
    Changes: Source and taxonomy
  • Version 1.4: 2017-07-05
    Changes: Data collection
  • Version 1.5: 2019-10-09
    Changes: Data collection, Experimental preparation, Other
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Refinement description