Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage.

Abstract

A 4 A electron-density map of Pf1 filamentous bacterial virus has been calculated from x-ray fiber diffraction data by using the maximum-entropy method. This method produces a map that is free of features due to noise in the data and enables incomplete isomorphous-derivative phase information to be supplemented by information about the nature of the solution. The map shows gently curved (banana-shaped) rods of density about 70 A long, oriented roughly parallel to the virion axis but slewing by about 1/6th turn while running from a radius of 28 A to one of 13 A. Within these rods, there is a helical periodicity with a pitch of 5 to 6 A. We interpret these rods to be the helical subunits of the virion. The position of strongly diffracted intensity on the x-ray fiber pattern shows that the basic helix of the virion is right handed and that neighboring nearly parallel protein helices cross one another in an unusual negative sense.Two structural classes of filamentous bacterial viruses have been identified (1). Class 1, exemplified by the fd (= fl = M 13) species, has been extensively studied by biochemical and genetic techniques whereas class 2, exemplified by the Pfl species, gives higher resolution x-ray fiber diffraction data and has been intensively studied by structural techniques (reviewed in refs. 2 and 3). Both classes of virion have a cylindrical protein coat of 60 A average outer diameter and 20 A average inner diameter encapsulating a single-stranded circular DNA molecule that stretches down the length of the central hole. The protein coat is essentially a helical array of several thousand identical protein units, although there are minor proteins at the ends of the virion that make up about 1% by weight of the coat.

Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages

“…The development of methods using the diamagnetic anisotropy of lnovirus to improve alignment in fibres (Nave et al, 1979;Torbet & Maret, 1979;Maret & Dransfeld, 1985) enabled closely spaced layer lines to be resolved and small intensity differences between native and heavy-atom derivative vir.iorus to be measured. These experimental advances enabled resolution of the symmetry ambiguities (Banner et al, 1981;Bryan et al, 1983;Bryan, 1987;Marvin et al, 1987;Glucksman et ai., 1992). The subunit axis follows a right-handed helix; the virion helix symmetry obeys q = 5; and class I can be described as a step-"function perturbation of the class II helix.…”

The molecular structure and structural transition of the α-helical capsid in filamentous bacteriophage Pf1

“…The ambiguities were eventually fully resolved using higher resolution diffraction data from native virions and heavy-atom derivatives, and using a maximumentropy method to calculate a model-independent electrondensity distribution (Nave et al, 1979Marvin et al, 1981Marvin et al, , 1987Bryan et al, 1983;, enabling a molecular model to be built and re®ned against the quantitative X-ray data (Bryan et al, 1983;Marvin, 1990a,b;Marvin et al, 1992;Gonzalez et al, 1995). The canonical class II Pf1 virion has 27 subunits in ®ve turns of a right-handed helix with an axial repeat c of about 75±80 A Ê (c varies slightly with the water content of the ®bre; Marvin et al, 1974).…”

Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR

“…All three of these Pf1 L models use the same helix parameters relating identical points in each subunit to the next within the virion helix: a positive unit twist 65.915° around the virion axis and a unit rise 3.05 Å parallel to the virion axis (Bryan et al 1983). We index subunits along this basic helix, starting from any arbitrary subunit indexed as k = 0, so the cylindrical polar coordinates of the k th subunit are φ = 65.915 k ° and z = 3.05 k Å.…”