Protein-nucleic acid interactions in the Tobacco virus.(2tmv)
Tobacco Mosaic Virus
Tobacco Mosaic Virus (TMV) is composed of 2130 identical coat protein subunits following the
right-handed helix of an accompanying RNA strand to produce a 300 nm hollow cylinder with an
outer diameter of 18 nm and a 4 nm wide central channel.
Caspar Carboxylates
Two clusters of acidic amino acids are thought to be important for the disassembly of the . When the virus enters cells, the higher pH and lower calcium levels increase the repulsion of neighboring carboxylates, destabilizing the capsid. This concept was originally proposed by Caspar and subsequently examined by site-directed mutagenesis [1]. Several carboxylates were identified including , which contact each other in the helical stack (look closely at the in this lockwasher complex), and a cluster of four acidic amino acids, , near the center of the ring.
This section complements the article on Tobacco Mosaic Virus in the
Molecule of the Month Series. See also Teaching Scenes, Tutorials, and Educators' Pages.
Repeating Subunits
Th repeating basic unit consists of 49 subunits which cover a section of 69 Å of height in three turns of the helix (= a rise of 23 Å per turn). A single strand of RNA is placed between the protein subunits at a distance of 40 Å from the outer diameter. The figure depicts one basic unit. Protein and RNA are shown in spacefill mode, RNA in white, the protein changing from red to blue along the helix. The uppermoust subunit is marked light brown. Each protein subunit covers three nucleotides of the RNA.
Repeating Subunits of Helical Tobacco Mosaic Virus
Publication Abstract from PubMed
The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71 water molecules, and two calcium-binding sites. Viral disassembly is driven by electrostatic repulsions between the charges in two carboxyl-carboxylate pairs and a phosphate-carboxylate pair. The phosphate-carboxylate pair and at least one of the carboxyl-carboxylate pairs appear to be calcium-binding sites. Nucleotide specificity, enabling TMV to recognize its own RNA by a repeating pattern of guanine residues, is provided by two guanine-specific hydrogen bonds in one of the three base-binding sites.
Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction., Namba K, Pattanayek R, Stubbs G, J Mol Biol. 1989 Jul 20;208(2):307-25. PMID:2769760
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2TMV is a 2 chains structure with sequences from Tobacco mosaic virus. The January 2009 RCSB PDB Molecule of the Month feature on Tobacco Mosaic Virus by David Goodsell is 10.2210/rcsb_pdb/mom_2009_1. Full crystallographic information is available from OCA.
