PDBsum entry 1ddl

Virus/RNA

PDB id: 1ddl

Contents

Protein chains

188 a.a. *

175 a.a. *

DNA/RNA

Ligands

__U-__U

Waters ×285

* Residue conservation analysis

PDB id:

1ddl

Name:

Virus/RNA

Title:

Desmodium yellow mottle tymovirus

Structure:

RNA (5'-r(p Up Up Up Up Up Up U)-3'). Chain: d. Fragment: viral RNA fragment. Engineered: yes. RNA (5'-r(p Up U)-3'). Chain: e. Fragment: viral RNA fragment. Engineered: yes. Desmodium yellow mottle virus.

Source:

Synthetic: yes. Desmodium yellow mottle virus. Organism_taxid: 70821

Resolution:

2.70Å R-factor: 0.151 R-free: 0.159

Authors:

S.B.Larson,J.Day,M.A.Canady,A.Greenwood,A.Mcpherson

Key ref:

S.B.Larson et al. (2000). Refined structure of desmodium yellow mottle tymovirus at 2.7 A resolution. J Mol Biol, 301, 625-642. PubMed id: 10966774 DOI: 10.1006/jmbi.2000.3983

Date:

10-Nov-99 Release date: 30-Oct-00

Protein chains

O89511  (O89511_9VIRU) -  Coat protein from Desmodium yellow mottle virus

Seq: 188 a.a.

Struc: 188 a.a.

Protein chain

O89511  (O89511_9VIRU) -  Coat protein from Desmodium yellow mottle virus

Seq: 188 a.a.

Struc: 175 a.a.

DNA/RNA chain

U-U-U-U-U-U-U 7 bases

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.?

DOI no: 10.1006/jmbi.2000.3983

J Mol Biol 301:625-642 (2000)

PubMed id: 10966774

Refined structure of desmodium yellow mottle tymovirus at 2.7 A resolution.

S.B.Larson, J.Day, M.A.Canady, A.Greenwood, A.McPherson.

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 625-642) copyright 2000.

Figures were selected by an automated process.