3J06

CryoEM Helical Reconstruction of TMV

Summary for 3J06

• Entry DOI: 10.2210/pdb3j06/pdb
• EMDB information: 5185
• Descriptor: Coat protein, 5'-R(P*AP*UP*G)-3' (2 entities in total)
• Functional Keywords: rna, virus
• Biological source: Tobacco mosaic virus; More
• Total number of polymer chains: 2
• Total formula weight: 18572.24

Authors

Ge, P.,Zhou, Z.H. (deposition date: 2011-04-26, release date: 2011-06-01, Last modification date: 2024-02-21)

Primary citation

Ge, P.,Zhou, Z.H.
Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches.
Proc.Natl.Acad.Sci.USA, 108:9637-9642, 2011

PubMed Abstract: Helical assemblies such as filamentous viruses, flagella, and F-actin represent an important category of structures in biology. As the first discovered virus, tobacco mosaic virus (TMV) was at the center of virus research. Previously, the structure of TMV was solved at atomic detail by X-ray fiber diffraction but only for its dormant or high-calcium-concentration state, not its low-calcium-concentration state, which is relevant to viral assembly and disassembly inside host cells. Here we report a helical reconstruction of TMV in its calcium-free, metastable assembling state at 3.3 Å resolution by cryo electron microscopy, revealing both protein side chains and RNA bases. An atomic model was built de novo showing marked differences from the high-calcium, dormant-state structure. Although it could be argued that there might be inaccuracies in the latter structure derived from X-ray fiber diffraction, these differences can be interpreted as conformational changes effected by calcium-driven switches, a common regulatory mechanism in plant viruses. Our comparisons of the structures of the low- and high-calcium states indicate that hydrogen bonds formed by Asp116 and Arg92 in the place of the calcium ion of the dormant (high-calcium) state might trigger allosteric changes in the RNA base-binding pockets of the coat protein. In turn, the coat protein-RNA interactions in our structure favor an adenine-X-guanine (A*G) motif over the G*A motif of the dormant state, thus offering an explanation underlying viral assembly initiation by an AAG motif.

PubMed: 21586634
DOI: 10.1073/pnas.1018104108

Experimental method

ELECTRON MICROSCOPY (3.3 Å)