1YC6

Crystallographic Structure of the T=1 Particle of Brome Mosaic Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallographic structure of the T=1 particle of brome mosaic virus.

Larson, S.B.Lucas, R.W.McPherson, A.

(2005) J Mol Biol 346: 815-831

  • DOI: 10.1016/j.jmb.2004.12.015
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • T=1 icosahedral particles of amino terminally truncated brome mosaic virus (BMV) protein were created by treatment of the wild-type T=3 virus with 1M CaCl2 and crystallized from sodium malonate. Diffraction data were collected from frozen crystals to ...

    T=1 icosahedral particles of amino terminally truncated brome mosaic virus (BMV) protein were created by treatment of the wild-type T=3 virus with 1M CaCl2 and crystallized from sodium malonate. Diffraction data were collected from frozen crystals to beyond 2.9 A resolution and the structure determined by molecular replacement and phase extension. The particles are composed of pentameric capsomeres from the wild-type virions which have reoriented with respect to the original particle pentameric axes by rotations of 37 degrees , and formed tenuous interactions with one another, principally through conformationally altered C-terminal polypeptides. Otherwise, the pentamers are virtually superimposable upon those of the original T=3 BMV particles. The T=1 particles, in the crystals, are not perfect icosahedra, but deviate slightly from exact symmetry, possibly due to packing interactions. This suggests that the T=1 particles are deformable, which is consistent with the loose arrangement of pentamers and latticework of holes that penetrate the surface. Atomic force microscopy showed that the T=3 to T=1 transition could occur by shedding of hexameric capsomeres and restructuring of remaining pentamers accompanied by direct condensation. Knowledge of the structures of the BMV wild-type and T=1 particles now permit us to propose a tentative model for that process. A comparison of the BMV T=1 particles was made with the reassembled T=1 particles produced from the coat protein of trypsin treated alfalfa mosaic virus (AlMV), another bromovirus. There is little resemblance between the two particles. The BMV particle, with a maximum diameter of 195 A, is made from distinctive pentameric capsomeres with large holes along the 3-fold axis, while the AlMV particle, of approximate maximum diameter 220 A, has subunits closely packed around the 3-fold axis, large holes along the 5-fold axis, and few contacts within pentamers. In both particles crucial linkages are made about icosahedral dyads.


    Related Citations: 
    • THE CRYSTALLOGRAPHIC STRUCTURE OF BROME MOSAIC VIRUS
      Lucas, R.W., Larson, S.B., McPherson, A.
      (2002) J Mol Biol 317: 95
    • CRYSTALLIZATION OF BROME MOSAIC VIRUS AND T=1 BROME MOSAIC VIRUS PARTICLES FOLLOWING A STRUCTURAL TRANSITION
      Lucas, R.W., Kuznetsov, Y.G., Larson, S.B., McPherson, A.
      (2001) Virology 286: 290

    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coat protein1, 2, 3, 4, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z154Brome mosaic virusMutation(s): 0 
Gene Names: ORF3b
Find proteins for P03602 (Brome mosaic virus)
Explore P03602 
Go to UniProtKB:  P03602
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.77α = 90
b = 194.77β = 90
c = 428.94γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SDMSdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance