2VQ0 | pdb_00002vq0

Capsid structure of Sesbania mosaic virus coat protein deletion mutant rCP(delta 48 to 59)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.258 (Depositor) 
  • R-Value Work: 
    0.257 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2VQ0

This is version 1.4 of the entry. See complete history

Literature

Structure of Recombinant Capsids Formed by the Beta-Annulus Deletion Mutant-Rcp (Delta 48-59) of Sesbania Mosaic Virus

Anju, P.Subashchandrabose, C.Satheshkumar, P.S.Savithri, H.S.Murthy, M.R.N.

(2008) Virology 375: 190

  • DOI: https://doi.org/10.1016/j.virol.2008.01.023
  • Primary Citation Related Structures: 
    2VQ0

  • PubMed Abstract: 

    A unique feature of several T=3 icosahedral viruses is the presence of a structure called the beta-annulus formed by extensive hydrogen bonding between protein subunits related by icosahedral three-fold axis of symmetry. This unique structure has been suggested as a molecular switch that determines the T=3 capsid assembly. In order to examine the importance of the beta-annulus, a deletion mutant of Sesbania mosaic virus coat protein in which residues 48-59 involved in the formation of the beta-annulus were deleted retaining the rest of the residues in the amino terminal segment (rCP (Delta48-59)) was constructed. When expressed in Escherichia coli, the mutant protein assembled into virus like particles of sizes close to that of the wild type virus particles. The purified capsids were crystallized and their three dimensional structure was determined at 3.6 A resolution by X-ray crystallography. The mutant capsid structure closely resembled that of the native virus particles. However, surprisingly, the structure revealed that the assembly of the particles has proceeded without the formation of the beta-annulus. Therefore, the beta-annulus is not essential for T=3 capsid assembly as speculated earlier and may be formed as a consequence of the particle assembly. This is the first structural demonstration that the virus particle morphology with and without the beta-annulus could be closely similar.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560 012, India.

Macromolecule Content 

  • Total Structure Weight: 82.87 kDa 
  • Atom Count: 4,454 
  • Modeled Residue Count: 606 
  • Deposited Residue Count: 768 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COAT PROTEIN
A, B, C
256Sesbania mosaic virusMutation(s): 0 
UniProt
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.258 (Depositor) 
  • R-Value Work:  0.257 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: R 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 288.793α = 61.7
b = 288.793β = 61.7
c = 288.793γ = 61.7
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Other, Refinement description, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary