PDBsum entry 1f2n

Virus

PDB id: 1f2n

Contents

Protein chains

189 a.a. *

212 a.a. *

Metals

_CA ×3

Waters ×199

* Residue conservation analysis

PDB id:

1f2n

Name:

Virus

Title:

Rice yellow mottle virus

Structure:

Capsid protein. Chain: a, b, c. Other_details: collected from rice field in the ivory coast and was propagated under contained conditions in a susceptible rice variety ir8 (oryza sativa l.)

Source:

Rice yellow mottle virus. Organism_taxid: 31744

Resolution:

2.80Å R-factor: 0.218 R-free: 0.219

Authors:

C.Qu,L.Liljas,N.Opalka,C.Brugidou,M.Yeager,R.N.Beachy,C.M.Fauquet, J.E.Johnson,T.Lin

Key ref:

C.Qu et al. (2000). 3D domain swapping modulates the stability of members of an icosahedral virus group. Structure, 8, 1095-1103. PubMed id: 11080631 DOI: 10.1016/S0969-2126(00)00508-6

Date:

26-May-00 Release date: 01-Nov-00

Protein chains

Q86527  (Q86527_9VIRU) -  Capsid protein from Rice yellow mottle virus

Seq: 239 a.a.

Struc: 189 a.a.

Protein chain

Q86527  (Q86527_9VIRU) -  Capsid protein from Rice yellow mottle virus

Seq: 239 a.a.

Struc: 212 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.?

DOI no: 10.1016/S0969-2126(00)00508-6

Structure 8:1095-1103 (2000)

PubMed id: 11080631

3D domain swapping modulates the stability of members of an icosahedral virus group.

C.Qu, L.Liljas, N.Opalka, C.Brugidou, M.Yeager, R.N.Beachy, C.M.Fauquet, J.E.Johnson, T.Lin.

ABSTRACT

BACKGROUND: Rice yellow mottle virus (RYMV) is a major pathogen that dramatically reduces rice production in many African countries. RYMV belongs to the genus sobemovirus, one group of plant viruses with icosahedral capsids and single-stranded, positive-sense RNA genomes. RESULTS: The structure of RYMV was determined and refined to 2.8 A resolution by X-ray crystallography. The capsid contains 180 copies of the coat protein subunit arranged with T = 3 icosahedral symmetry. Each subunit adopts a jelly-roll beta sandwich fold. The RYMV capsid structure is similar to those of other sobemoviruses. When compared with these viruses, however, the betaA arm of the RYMV C subunit, which is a molecular switch that regulates quasi-equivalent subunit interactions, is swapped with the 2-fold-related betaA arm to a similar, noncovalent bonding environment. This exchange of identical structural elements across a symmetry axis is categorized as 3D domain swapping and produces long-range interactions throughout the icosahedral surface lattice. Biochemical analysis supports the notion that 3D domain swapping increases the stability of RYMV. CONCLUSIONS: The quasi-equivalent interactions between the RYMV proteins are regulated by the N-terminal ordered residues of the betaA arm, which functions as a molecular switch. Comparative analysis suggests that this molecular switch can also modulate the stability of the viral capsids.

Selected figure(s)

Figure 5.
Figure 5. Stereoviews of the RYMV bA Arm and the Calcium Binding Sites in Two Sobemoviruses.(a) The electron density of the peptide chain where the RYMV bA arm conformation differs from that of SCPMV. The electron density is shown as chickenwire and the polypeptide chain is in stick representation. The sequence Pro-Gly-Pro favors directional change of the peptide folding [23]. This figure was made using the program BOBSCRIPT [24]. The calcium binding site at the A-B subunit interface in (b) RYMV and (c) SCPMV. The A and B subunits are in blue and red, respectively. In (b), residues Asp126 and Asp129 in the A subunit and residues Val182, Asn237 and Thr238 in the B subunit are shown in ball-and-stick representation. In (c), residues Asp138 and Asp141 in the A subunit and residues Phe199, Asn259 and Leu260 are shown in ball-and-stick representation. Atoms of carbon, nitrogen and oxygen are in yellow, blue, and red, respectively. The calcium ions are drawn as 1Å spheres in magenta

The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1095-1103) copyright 2000.

Figure was selected by an automated process.