Summary information and primary citation
- PDB-id
-
1ddl;
DSSR-derived features in text and
JSON formats; DNAproDB
- Class
- virus-RNA
- Method
- X-ray (2.7 Å)
- Summary
- Desmodium yellow mottle tymovirus
- Reference
-
Larson SB, Day J, Canady MA, Greenwood A, McPherson A
(2000): "Refined
structure of desmodium yellow mottle tymovirus at 2.7 A
resolution." J.Mol.Biol.,
301, 625-642. doi: 10.1006/jmbi.2000.3983.
- Abstract
- Desmodium yellow mottle virus is a 28 nm diameter, T=3
icosahedral plant virus of the tymovirus group. Its
structure has been solved to a resolution of 2.7 A using
X-ray diffraction analysis based on molecular replacement
and phase extension methods. The final R value was 0.151
(R(free)=0.159) for 134,454 independent reflections. The
folding of the polypeptide backbone is nearly identical
with that of turnip yellow mosaic virus, as is the
arrangement of subunits in the virus capsid. However, a
major difference in the disposition of the amino-terminal
ends of the subunits was observed. In turnip yellow mosaic
virus, those from the B and C subunits comprising the
hexameric capsomeres formed an annulus about the interior
of the capsomere, while the corresponding N termini of the
pentameric capsomere A subunits were not visible at all in
electron density maps. In Desmodium yellow mottle
tymovirus, amino termini from the A and B subunits combine
to form the annuli, thereby resulting in a much
strengthened association between the two types of
capsomeres and an, apparently, more stable capsid. The
first 13 residues of the C subunit were invisible in
electron density maps. Two ordered fragments of
single-stranded RNA, seven and two nucleotides in length,
were observed. The ordered water structure of the virus
particle was delineated and required 95 solvent molecules
per protein subunit.
