Enzymind Labs

P22 virion structure, EMD-1220 rendering notes

[2008-09-10 Note: After I did the following renderings, I was pointed to an even better data set of the same virion. See P22 virion structure, EMD-1220 rendering notes.]

Steve McQuinn pointed out an interesting volume data set of a virion, below are a few renderings. If you wanted to make a self-assembling machine, this might be a good place to start. [Also see Steve McQuinn's T4 phage contractile tail sheath rendering.]

This is the virion of P22, a bacteriophage. A virion is the infectious form of a virus as it exists outside the host cell, consisting of a nucleic acid core, and a protein coat. At left is a surface rendering, and at right 2-D slices along the axis.

It's striking that the business end (tail complex) has hexagonal symmetry but the body (capsid) is pentagonal (an icosahedron). How many molecules or base units make up the visible "kinks"? The paper below has a great explanation of many facets of the concentric ring structures (composed of dsDNA) and the tail structures.

J.Chang, P.Weigele, J.King, W.Chiu, W.Jiang:
Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure (2006) 14, pp. 1073-1082 [PubMed entry 16730179]

Abstract:

"The mechanisms by which most double-stranded DNA viruses package and release their genomic DNA are not fully understood. Single particle cryo-electron microscopy and asymmetric 3D reconstruction reveal the organization of the complete bacteriophage P22 virion, including the protein channel through which DNA is first packaged and later ejected. This channel is formed by a dodecamer of portal proteins and sealed by a tail hub consisting of two stacked barrels capped by a protein needle. Six trimeric tailspikes attached around this tail hub are kinked, suggesting a functional hinge that may be used to trigger DNA release. Inside the capsid, the portal's central channel is plugged by densities interpreted as pilot/injection proteins. A short rod-like density near these proteins may be the terminal segment of the dsDNA genome. The coaxially packed DNA genome is encapsidated by the icosahedral shell. This complete structure unifies various biochemical, genetic, and crystallographic data of its components from the past several decades."

Data source: EMD_1222, Macromolecular Structure Database.

Also see National Center for Macromolecular Imaging 's "Movie S1. Animation of the Asymmetric Reconstruction of Bacteriophage P22 Illustrating the Dispositions of the Different Structural Components".

(Larger version of below)