PDBsum entry 1ql1

Virus

PDB id: 1ql1

Contents

Protein chain

46 a.a.

PDB id:

1ql1

Name:

Virus

Title:

Inovirus (filamentous bacteriophage) strain pf1 major coat protein assembly

Structure:

Pf1 bacteriophage coat protein b. Chain: a. Synonym: pf1 inovirus. Engineered: yes. Other_details: major coat protein assembly in the higher-temperature symmetry

Source:

Pseudomonas phage pf1. Organism_taxid: 10871. Expressed in: pseudomonas aeruginosa. Expression_system_taxid: 287. Other_details: grown in pseudomonas aeruginosa

Authors:

L.C.Welsh,M.F.Symmons,D.A.Marvin

Key ref:

L.C.Welsh et al. (2000). The molecular structure and structural transition of the alpha-helical capsid in filamentous bacteriophage Pf1. Acta Crystallogr D Biol Crystallogr, 56, 137-150. PubMed id: 10666593 DOI: 10.1107/S0907444999015334

Date:

20-Aug-99 Release date: 07-Feb-00

Protein chain

P03621  (CAPSD_BPPF1) -  Capsid protein G8P from Pseudomonas phage Pf1

Seq: 82 a.a.

Struc: 46 a.a.

DOI no: 10.1107/S0907444999015334

Acta Crystallogr D Biol Crystallogr 56:137-150 (2000)

PubMed id: 10666593

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

L.C.Welsh, M.F.Symmons, D.A.Marvin.

ABSTRACT

The major coat protein in the capsid of Pf1 filamentous bacteriophage (Inovirus) forms a helical assembly of about 7000 identical protein subunits, each of which contains 46 amino-acid residues and can be closely approximated by a single gently curved alpha-helix. Since the viral DNA occupies the core of the tubular capsid and appears to make no significant specific interactions with the capsid proteins, the capsid is a simple model system for the study of the static and dynamic properties of alpha-helix assembly. The capsid undergoes a reversible temperature-induced structural transition at about 283 K between two slightly different helix forms. The two forms can coexist without an intermediate state, consistent with a first-order structural phase transition. The molecular model of the higher temperature form was refined using improved X-ray fibre diffraction data and new refinement and validation methods. The refinement indicates that the two forms are related by a change in the orientation of the capsid subunits within the virion, without a significant change in local conformation of the subunits. On the higher temperature diffraction pattern there is a region of observed intensity that is not consistent with a simple helix of identical subunits; it is proposed that the structure involves groups of three subunits which each have a slightly different orientation within the group. The grouping of subunits suggests that a change in subunit libration frequency could be the basis of the Pf1 structural transition; calculations from the model are used to explore this idea.

Selected figure(s)

Figure 3.
Figure 3 The Pf1^L subunit 4ifm (solid lines) and the Pf1^H subunit 2ifn (broken lines). The relative position of model 4ifm was altered by rotating and translating the coordinates with respect to the virion axis in order to superimpose the centres of the subunits. Lines connect C^ atoms. Steroview from outside the virion towards the virion axis, which is shown as a vertical line.

Figure 8.
Figure 8 Grouping of subunits in the perturbed helix. Views perpendicular to the virion axis, N-termini of the subunits towards the top. Colour coding as in Fig. 6-. (a) Units k = 1 and k = 2 in the virion basic helix are superposed on unit k = 0 by the operation (-kTH, -kHH). Black, model RPf1^H; red, unit k = 0 of model 3RPf1^H; green, k = 1; blue, k = 2. Heavy lines connect C^ atoms; lighter lines connect side-chain non-H atoms. Stereoview from outside the virion towards the virion axis, which is shown as a vertical line. (b) Models as (a) but viewed at 90° to (a), tangent to the circumference of a cylinder coaxial with the virion, in the direction of increasing cylindrical polar angle . (c) The assembly of subunits in model 3RPf1^H. Each subunit is represented as a space-filling coil following the protein backbone at 5 Å radius. Axial slab about 100 Å long, corresponding to about 0.5% of the total length of the virion. Colour coding as in (a): red, k = 0, 3, 6, 9, ...; green, k = 1, 4, 7, 10, ...; blue, k = 2, 5, 8, 11, ... . Three adjacent subunits (k = 0, -6, -11) are shown in atomic detail (white lines) within `transparent' rods. Heavy lines connect C^ atoms; lighter lines connect side-chain non-H atoms.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 137-150) copyright 2000.

Figures were selected by the author.