PDBsum entry 2vvf

Viral protein

PDB id: 2vvf

Contents

Protein chains

(+ 0 more) 269 a.a. *

Metals

_CA ×6

Waters ×181

* Residue conservation analysis

PDB id:

2vvf

Name:

Viral protein

Title:

Crystal structure of the major capsid protein p2 from bacteriophage pm2

Structure:

Major capsid protein p2. Chain: a, b, c, d, e, f. Synonym: p2 major capsid protein

Source:

Pseudoalteromonas phage pm2. Pm2. Organism_taxid: 10661

Resolution:

2.50Å R-factor: 0.241 R-free: 0.258

Authors:

N.G.A.Abrescia,J.M.Grimes,H.K.Kivela,R.Assenberg,G.C.Sutton, S.J.Butcher,J.K.H.Bamford,D.H.Bamford,D.I.Stuart

Key ref:

N.G.Abrescia et al. (2008). Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Mol Cell, 31, 749-761. PubMed id: 18775333 DOI: 10.1016/j.molcel.2008.06.026

Date:

06-Jun-08 Release date: 16-Sep-08

Protein chains

P15794  (CAPSD_BPPM2) -  Major capsid protein P2 from Pseudoalteromonas phage PM2

Seq: 269 a.a.

Struc: 269 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.molcel.2008.06.026

Mol Cell 31:749-761 (2008)

PubMed id: 18775333

Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2.

N.G.Abrescia, J.M.Grimes, H.M.Kivelä, R.Assenberg, G.C.Sutton, S.J.Butcher, J.K.Bamford, D.H.Bamford, D.I.Stuart.

ABSTRACT

Recent, primarily structural observations indicate that related viruses, harboring no sequence similarity, infect hosts of different domains of life. One such clade of viruses, defined by common capsid architecture and coat protein fold, is the so-called PRD1-adenovirus lineage. Here we report the structure of the marine lipid-containing bacteriophage PM2 determined by crystallographic analyses of the entire approximately 45 MDa virion and of the outer coat proteins P1 and P2, revealing PM2 to be a primeval member of the PRD1-adenovirus lineage with an icosahedral shell and canonical double beta barrel major coat protein. The view of the lipid bilayer, richly decorated with membrane proteins, constitutes a rare visualization of an in vivo membrane. The viral membrane proteins P3 and P6 are organized into a lattice, suggesting a possible assembly pathway to produce the mature virus.

Selected figure(s)

Figure 5.
Figure 5. Proteins P3 and P6
(A and B) Stereo pictures of contiguous views of a portion of Cα traces of a P3 dimer (magenta) and P6 (gold) fitted in the virus map (0.7σ, blue), with SeMet difference Fourier (3.2σ, red) viewed orthogonally to the virus surface.

Figure 6.
Figure 6. Membrane and Genome Architecture
(A) (Left) Slice through the PM2 electron density. The capsid is blue (0.8σ), lipid headgroups cyan (0.25σ), acyl-chain region light red (−1.3σ), and supercoiled DNA green (0.25σ). (Right) Icosahedral electron density profile. Distances measured from the particle center along the icosahedral 3-fold axis. IL and OL mark the inner and outer membrane leaflets, respectively.
(B) Cartoon of PM2 membrane vesicle assembly. (1) Dimers of protein P3 (magenta) and a monomer of protein P6 (gold) anchored via transmembrane helices (data not shown) on a patch of bacterial membrane. (2) Independent P3 dimers interact with monomeric P6 forming the scaffold building block. (3) Three building blocks come together by interaction of the P3 α1 helices to form a subassembly corresponding to an icosahedral facet. (4) P6 molecules of two independent subassemblies interact, facilitated by interaction with the supercoiled DNA genome via P6 transmembrane helices (and possibly further components such as P4). (5) This interaction generates a torque across the membrane via the P6 helices (depicted as small gold-colored rectangles), driving the curvature of the membrane. (6) Recruitment of further P6-P3 subassemblies to the condensed DNA genome leads to a correctly sized lipid vesicle coated with P3 and P6, on which the outer protein capsid assembles.

The above figures are reprinted by permission from Cell Press: Mol Cell (2008, 31, 749-761) copyright 2008.

Figures were selected by an automated process.