2om3

From Proteopedia

High-resolution cryo-EM structure of Tobacco Mosaic Virus

2om3, resolution 4.40Å

Structural highlights

2om3 is a 2 chain structure with sequence 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. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 4.4Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q77LT8_9VIRU

Evolutionary Conservation

Checkto colour the structure by Evolutionary Conservation, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.

High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.,Sachse C, Chen JZ, Coureux PD, Stroupe ME, Fandrich M, Grigorieff N J Mol Biol. 2007 Aug 17;371(3):812-35. Epub 2007 Jun 4. PMID:17585939^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sachse C, Chen JZ, Coureux PD, Stroupe ME, Fandrich M, Grigorieff N. High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus. J Mol Biol. 2007 Aug 17;371(3):812-35. Epub 2007 Jun 4. PMID:17585939 doi:10.1016/j.jmb.2007.05.088