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PDBsum entry 1ddl
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Refined structure of desmodium yellow mottle tymovirus at 2.7 a resolution.
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Authors
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S.B.Larson,
J.Day,
M.A.Canady,
A.Greenwood,
A.Mcpherson.
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Ref.
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J Mol Biol, 2000,
301,
625-642.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 5.
Figure 5. The N termini of (a) DYMV and (b) TYMV are viewed
along the quasi 3-fold axis of the respective ABC trimers
superimposed on the density of an (F[o] - F[c]) exp ia[c] omit
map with residues 15 to 26 of all subunits omitted from the
models. These maps demonstrate the validity of the differences
seen in the dispositions of the N termini of the two viruses.
The maps in (a) are contoured at 1.2s (cyan) and 0.8s (light
blue). The map in (b) is contoured at 2s.
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Figure 10.
Figure 10. (a) The location of the RNA fragments with
respect to the ABC trimer and (b), the location of RNA-A inside
the hexameric cavity. RNA-A is shown as white, RNA-B as cyan.
RNA-A lies along the inner surface between the annulus and the
quasi 3-fold axis.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
301,
625-642)
copyright 2000.
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