4V99

The Crystallographic Structure of Panicum Mosaic Virus

This is a non-PDB format compatible entry.

Summary for 4V99

• Entry DOI: 10.2210/pdb4v99/pdb
• Descriptor: Capsid protein, 5'-R(P*UP*UP*AP*AP*UP*AP*UP*UP*UP*UP*UP*AP*UP*UP*UP*UP*U)-3', CALCIUM ION (3 entities in total)
• Functional Keywords: icosahedral virus, tombusviridae, rna hairpin, virus coat protein, swiss jelly roll fold, virus-rna complex, virus/rna
• Biological source: Panicum mosaic virus (PMV); More
• Cellular location: Virion : P89036
• Total number of polymer chains: 480
• Total formula weight: 10135474.92

Authors

Makino, D.L.,Larson, S.B.,McPherson, A. (deposition date: 2012-07-04, release date: 2014-07-09, Last modification date: 2023-09-20)

Primary citation

Makino, D.L.,Larson, S.B.,McPherson, A.
The crystallographic structure of Panicum Mosaic Virus (PMV).
J.Struct.Biol., 181:37-52, 2013

PubMed Abstract: The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ∼20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca(++) ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1-53, 1-49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent "arm" that intertwines with symmetry equivalent "arms" at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A-B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses.

PubMed: 23123270
DOI: 10.1016/j.jsb.2012.10.012

Experimental method

X-RAY DIFFRACTION (2.9 Å)