PDBsum entry 1ql1

Virus

PDB id: 1ql1

Contents

Protein chain

46 a.a.

References listed in PDB file

Key reference

Title

The molecular structure and structural transition of the alpha-Helical capsid in filamentous bacteriophage pf1.

Authors

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

Ref.

Acta Crystallogr D Biol Crystallogr, 2000, 56, 137-150. [DOI no: 10.1107/S0907444999015334]

PubMed id

10666593

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.

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.

Secondary reference #1

Title

Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 a resolution X-Ray fibre diffraction data.

Authors

A.Gonzalez, C.Nave, D.A.Marvin.

Ref.

Acta Crystallogr D Biol Crystallogr, 1995, 51, 792-804. [DOI no: 10.1107/S0907444995003027]

PubMed id

15299811

Figure 2.
Fig. 2.21:o ­ F,. omit map of model SAR. Residues 16­19 were omitted from the model used to upply phases for calculating the map. The omt model was refined to reduce bias as described in §2.4. View aproximately as Fig. l(b), but broader to include not only the k = 0 uni (centre) but also the k =­­6 unit (left) and the k =­­11 uit (right). Electron density s contoured at 0.5 e,~­­~. (Stereo pair.)

Figure 5.
Fig. 5. Subunit of model SAR (heavy lines), shown together with parts of symmetry­related neighbouring subunits (light lines). Series of diagrams with the view drection prallel to the viron axis Each view direction is from larger towards smaller z and from smaller towards larger residue number away from the viewer; he series, (a) to (e), moves towards smaller z. The inside of the virion is towards the top of the figure and the outside towards th bottom. Amino acids are coded as follows. RESn is near the C of residue n in the reference asymmetric unit. RESmn is near the C ~ of residue n in symmetry­elated neighbour with index m, where m is 1 or the k = ­ 17 subunit; 2 for ­ 11; 3 for ­6; 4 for ­5; 5 fo ­ 1; for +1; 7 for +5; 8 for +6; 9 for +11; and 0 for +17. (Stereo pairs.)

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

Two forms of pf1 inovirus: X-Ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit

Authors

D.A.Marvin, C.Nave, M.Bansal, R.D.Hale, E.K.H.Salje.

Ref.

phase transitions, 1992, 39, 45.

Secondary reference #3

Title

Model-Building studies of inovirus: genetic variations on a geometric theme.

Author

D.A.Marvin.

Ref.

Int J Biol Macromol, 1990, 12, 125-138. [DOI no: 10.1016/0141-8130(90)90064-H]

PubMed id

2078529

Secondary reference #4

Title

Dynamics of telescoping inovirus: a mechanism for assembly at membrane adhesions.

Author

D.A.Marvin.

Ref.

Int J Biol Macromol, 1989, 11, 159-164.

PubMed id

2489076