PDBsum entry: 1gw8

Virus/viral protein

PDB id: 1gw8

Contents

Protein chains

(+ 6 more) 370 a.a.

PDB id:

1gw8

Name:

Virus/viral protein

Title:

Quasi-atomic resolution model of bacteriophage prd1 sus607 mutant, obtained by combined cryo-em and x-ray crystallography.

Structure:

Major capsid protein. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: protein p3. Engineered: yes. Other_details: sus607 mutant lacks the viral membrane aggregation protein p11

Source:

Bacteriophage prd1. Organism_taxid: 10658. Expressed in: salmonella typhimurium. Expression_system_taxid: 602.

Authors:

C.San Martin,J.Huiskonen,J.K.H.Bamford,S.J.Butcher, S.D.Fuller,D.H.Bamford,R.M.Burnett

Key ref:

C.San Martín et al. (2002). Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. Nat Struct Biol, 9, 756-763. PubMed id: 12219080 DOI: 10.1038/nsb837

Date:

08-Mar-02 Release date: 15-Mar-02

Protein chains

P22535  (CAPSD_BPPRD) -  Major capsid protein P3

Seq: 395 a.a.

Struc: 370 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: virion (2 terms)
• Biochemical function: structural molecule activity (1 term)

DOI no: 10.1038/nsb837

Nat Struct Biol 9:756-763 (2002)

PubMed id: 12219080

Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid.

C.San Martín, J.T.Huiskonen, J.K.Bamford, S.J.Butcher, S.D.Fuller, D.H.Bamford, R.M.Burnett.

ABSTRACT

Bacteriophage PRD1 shares many structural and functional similarities with adenovirus. A major difference is the PRD1 internal membrane, which acts in concert with vertex proteins to translocate the phage genome into the host. Multiresolution models of the PRD1 capsid, together with genetic analyses, provide fine details of the molecular interactions associated with particle stability and membrane dynamics. The N- and C-termini of the major coat protein (P3), which are required for capsid assembly, act as conformational switches bridging capsid to membrane and linking P3 trimers. Electrostatic P3-membrane interactions increase virion stability upon DNA packaging. Newly revealed proteins suggest how the metastable vertex works and how the capsid edges are stabilized.

Selected figure(s)

Figure 2.
Figure 2. Location of difference peaks in the PRD1 capsid. a, Surface rendering of the wt cryo-EM map, showing the location of icosahedral symmetry axes and the four independent positions in the asymmetric unit. Surface rendering of the difference maps superimposed on the X-ray derived maps (light blue) for b, wt; c, sus1; and d, the P3-shell. Note that the asymmetric unit is shown as seen from inside the virus, that is rotated 180° with respect to (a). The sus607 difference map (not shown) presented the same peaks as wt. The P3 trimers are labeled 1 -4 according to their position in the asymmetric unit. The difference map peaks are colored as follows: dark blue are type I peaks; red, type II; green, type III; gray, type IV; and yellow, vertex and membrane remnants after icosahedral masking. Darker tones highlight the peaks in the asymmetric unit. The predicted positions for glue proteins are labeled with an asterisk. White pentagons, triangles and ovals indicate the positions of the icosahedral five-fold, three-fold and two-fold axes, and broken and closed black triangles indicate the positions of the two different local three-fold axes in the asymmetric unit. The bar represents 50 Å. The contour of each trimer in the asymmetric unit is outlined, and can be compared with e, which shows a ribbon diagram of the P3 trimer as seen from inside the capsid. P3 monomers are ramp-colored according to distance from the virus center (gold, red or green from closest to white at farthest), highlighting the N-terminal helices that face the viral membrane. f, Ribbon diagram of one of the monomers as seen in a section across the capsid. The blue, red and green ellipses show the positions of the difference image type I, II and III peaks relative to the P3 molecule. The two viral jelly rolls (V1 and V2) and the N- and C-termini and the I1B2 loop are indicated.

Figure 7.
Figure 7. Stabilizing interactions in the capsid. Schematic of an asymmetric unit and its closest P3 neighbors, showing the proposed cementing interactions. Orange symbols indicate the icosahedral and local symmetry axes as in Fig. 2. The four P3 trimers in the asymmetric unit are depicted as black hexagons and labeled 1 -4, and the P3 trimers in adjacent asymmetric units are gray and labeled with a superscript according to their asymmetric unit. Radial lines in each hexagon indicate the interface between P3 subunits in a trimer. Gaps between hexagons indicate the edges of the icosahedral facet. Blue circles represent the ordered P3 N-terminal helices that contact the membrane in sus1; green ellipses, the difference peaks attributed to glue proteins; red arrows, P3 C-terminal bridges within the facet; and yellow curved arrows, the possible involvement of other C-termini in intertrimer bridges or interactions with glue proteins. C-termini that are equidistant from two difference peaks are represented as dashed double curved arrows. The view is from outside the virion.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 756-763) copyright 2002.

Figures were selected by the author.