PDBsum entry 1vak

Virus

PDB id: 1vak

Contents

Protein chain

196 a.a. *

Metals

_CA

Waters ×106

* Residue conservation analysis

PDB id:

1vak

Name:

Virus

Title:

T=1 capsid structure of sesbania mosaic virus coat protein deletion mutant cp-n(delta)65

Structure:

Coat protein. Chain: a. Fragment: residues 66-268. Engineered: yes

Source:

Sesbania mosaic virus. Organism_taxid: 12558. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.05Å R-factor: 0.211 R-free: 0.214

Authors:

V.Sangita,G.L.Lokesh,P.S.Satheshkumer,C.S.Vijay,V.Saravanan, H.S.Savithri,M.R.Murthy

Key ref:

V.Sangita et al. (2004). T=1 capsid structures of Sesbania mosaic virus coat protein mutants: determinants of T=3 and T=1 capsid assembly. J Mol Biol, 342, 987-999. PubMed id: 15342251 DOI: 10.1016/j.jmb.2004.07.003

Date:

18-Feb-04 Release date: 23-Nov-04

Protein chain

Q9EB06  (Q9EB06_9VIRU) -  Capsid protein from Sesbania mosaic virus

Seq: 268 a.a.

Struc: 196 a.a.

DOI no: 10.1016/j.jmb.2004.07.003

J Mol Biol 342:987-999 (2004)

PubMed id: 15342251

T=1 capsid structures of Sesbania mosaic virus coat protein mutants: determinants of T=3 and T=1 capsid assembly.

V.Sangita, G.L.Lokesh, P.S.Satheshkumar, C.S.Vijay, V.Saravanan, H.S.Savithri, M.R.Murthy.

ABSTRACT

Sesbania mosaic virus particles consist of 180 coat protein subunits of 29kDa organized on a T=3 icosahedral lattice. N-terminal deletion mutants of coat protein that lack 36 (CP-NDelta36) and 65 (CP-NDelta65) residues from the N terminus, when expressed in Escherichia coli, produced similar T=1 capsids of approximate diameter 20nm. In contrast to the wild-type particles, these contain only 60 copies of the truncated protein subunits (T=1). CP-NDelta65 lacks the "beta-annulus" believed to be responsible for the error-free assembly of T=3 particles. Though the CP-NDelta36 mutant has the beta-annulus segment, it does not form a T=3 capsid, presumably because it lacks an arginine-rich motif found close to the amino terminus. Both CP-NDelta36 and CP-NDelta65 T=1 capsids retain many key features of the T=3 quaternary structure. Calcium binding geometries at the coat protein interfaces in these two particles are also nearly identical. When the conserved aspartate residues that coordinate the calcium, D146 and D149 in the CP-NDelta65, were mutated to asparagine (CP-NDelta65-D146N-D149N), the subunits assembled into T=1 particles but failed to bind calcium ions. The structure of this mutant revealed particles that were slightly expanded. The analysis of the structures of these mutant capsids suggests that although calcium binding contributes substantially to the stability of T=1 particles, it is not mandatory for their assembly. In contrast, the presence of a large fraction of the amino-terminal arm including sequences that precede the beta-annulus and the conserved D149 appear to be indispensable for the error-free assembly of T=3 particles.

Selected figure(s)

Figure 6.
Figure 6. Stereo view of calcium binding region in CP-ND65 (red) and the corresponding region in CP-ND65-D146N-D149N (blue). D146 and D149, which participate in calcium coordination in CP-ND65, have undergone changes in CP-ND65-D146N-D149N. The C-terminal residues, which also coordinate to calcium in CP-ND65, are disordered in CP-ND65-D146N-D149N and, hence, are not shown.

Figure 8.
Figure 8. Schematic illustration of the effects of deleting segments corresponding to the N-ARM and the b-annulus and mutations of residues contributing ligands to calcium on particle assembly. Space filling models of T=3 (native), T=1 (CP-ND65) and swollen T=1 (CP-ND65-D146N-D149N) capsids were generated using the refined coordinates of the subunits in the respective structures.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 987-999) copyright 2004.

Figures were selected by an automated process.