|
The structure of the bacteriophage phi X174 was examined in a 2.7 A resolution
map and refined, using 6.0 A to 3.0 A resolution data with F > or = 5 sigma
(F). The final R-factor was 20.9% and the root-mean-square deviation from
idealized bond lengths was 0.021 A. The Hendrickson-Konnert refinement was
restrained by the phases derived from the molecular replacement icosahedral
averaging procedure. The mature phage capsid consists of 60 copies of the F
protein with 426 amino acids, the G protein with 175 amino acids and the J
protein with 37 amino acids, as well as 12 copies of the H protein with 328
amino acids. The entire polypeptide chain of the F and G protein, all but the
first N-terminal residue of the J protein, and 178 solvent molecules were
included in the refinement calculations. The secondary structural features of
the F, G and J proteins and their interactions with each other are described.
The majority of the protein-protein interactions are between the icosahedral
5-fold related interfaces of the F and of the G proteins. These pentameric units
of the F and G proteins form the 9S and 6S assembly intermediates, respectively.
The J protein lacks any secondary structure and acts as a linking arm between
the icosahedral 5-fold related F proteins. Water molecules were introduced only
after phase extension to 2.7 A resolution had been completed. The F protein is
associated with lower "thermal" parameters and exhibits greater water order in
its environment than the G and J proteins. The largest thermal parameters occur
in residues on the viral surface. The solvent contributes to the interactions
between the proteins. There is an interface of solvent molecules between the F
and the G pentamers which stabilizes the pentameric G protein spikes in a crater
centered at each of the icosahedral 5-fold vertices of the F protein capsid.
Sequence alignments of the F, G and J amino acid sequences for the homologous
bacteriophages G4, alpha 3, phi K and phi X174 with respect to the phi X174
structure demonstrated the conservation of functionally important residues on
the viral surface.
|
