SNAP output for PDB entry 1pfi [SNAP web server]

PDB-id

1pfi; SNAP-derived features in text and JSON formats; DNAproDB

Class

virus

Method

fiber diffraction

Summary

Pf1 virus structure: helical coat protein and DNA with paraxial phosphates

Reference

Liu DJ, Day LA (1994): "Pf1 virus structure: helical coat protein and DNA with paraxial phosphates." Science, 265, 671-674.

Abstract

The helical path of the DNA in filamentous bacteriophage Pf1 was deduced from different kinds of existing structural information, including results from x-ray fiber diffraction. The DNA has the same pitch, 16 angstroms, as the surrounding helix of protein subunits; the rise and rotation per nucleotides are 6.1 angstroms and 132 degrees, respectively; and the phosphates are 2.5 angstroms from the axis. The DNA in Pf1 is, therefore, the most extended and twisted DNA structure known. On the basis of the DNA structure and extensive additional information about the protein, a model of the virion is proposed. In the model, the DNA bases reach out, into the protein, and the lysine and arginine side chains reach in, between the DNA bases, to stabilize the paraxial phosphate charges; the conformation of the protein subunit is a combination of alpha and 3(10) helices.