PDBsum entry 1upn

Virus/receptor

PDB id: 1upn

Contents

Protein chains

289 a.a. *

252 a.a. *

238 a.a. *

60 a.a. *

125 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The structure of echovirus type 12 bound to a two-Domain fragment of its cellular attachment protein decay-Accelerating factor (cd 55).

Authors

D.Bhella, I.G.Goodfellow, P.Roversi, D.Pettigrew, Y.Chaudhry, D.J.Evans, S.M.Lea.

Ref.

J Biol Chem, 2004, 279, 8325-8332. [DOI no: 10.1074/jbc.M311334200]

PubMed id

14634014

Abstract

Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.

Figure 2.
FIG. 2. Stereo pairs of surface rendered three-dimensional reconstructions of unlabeled EV12 virions (A) and DAF[34]-labeled virions (B). Isosurfaces of these reconstructions are merged and rendered in their respective color schemes to highlight the differences in density attributed to the two SCR domain fragment of DAF (C). A low resolution representation of EV7 bound to DAF[1234], derived from PDB code 1M11 [PDB] (30), highlights the differently oriented densities in these two complexes (D). In this model the densities of two copies of DAF[1234] are superimposed, laying across the virion 2-fold symmetry axes, giving rise to a hybrid density representing the two possible positions for the molecule. A radial depth-cue color scheme is used to indicate distance from the center of the virion (see the key).

Figure 5.
FIG. 5. A comparison of the low resolution three-dimensional reconstruction of EV12-DAF[34] (A) and a space-filling representation of the EV12-DAF[34] complex (B), generated using the crystallographic co-ordinates for EV11 and DAF[34]. Radial depth-cueing emphasizes the distance between atoms or regions of density and the center of the virion such that dark colors are close to the center and light colors are farther away. EV12 (and EV11) is colored in shades of blue, whereas DAF[34] is colored in green. A space-filling representation of the EV7-DAF[1234] complex (30) (C) highlights the different orientation of DAF bound to these two viruses. The model deposited under PDB code 1M11 [PDB] contains -carbon atoms only; this view is therefore rendered with the atomic radii for each atom set to 3.5Å. EV7 is colored in shades of purple, and the receptor is in red. A close-up view of DAF[34] shown as in panel B but rotated 180^o about a vertical axis exposes the residues buried in the virus-receptor complex (D). Residues are colored according to their contribution to the total contact area ( 840 Å2); yellow (1 < 5%), orange (5 < 9%), and red (9%+). A close-up view of EV11 without the receptor in place exposes buried residues on the surface of the capsid that are colored according to the same scheme (E); the biological protomer is indicated.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 8325-8332) copyright 2004.