PDBsum entry 1vpn

Viral protein

PDB id: 1vpn

Contents

Protein chains

285 a.a. *

Waters ×2096

* Residue conservation analysis

PDB id:

1vpn

Name:

Viral protein

Title:

Unassembled polyomavirus vp1 pentamer

Structure:

Polyomavirus vp1 pentamer. Chain: a, b, c, d, e. Engineered: yes

Source:

Murine polyomavirus. Organism_taxid: 10634. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Pentamer (from PDB file)

Resolution:

2.00Å R-factor: 0.176 R-free: 0.199

Authors:

T.Stehle,S.C.Harrison

Key ref:

T.Stehle and S.C.Harrison (1997). High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding. EMBO J, 16, 5139-5148. PubMed id: 9305654 DOI: 10.1093/emboj/16.16.5139

Date:

07-Mar-97 Release date: 15-May-97

Protein chains

P49302  (VP1_POVMP) -  Capsid protein VP1 from Murine polyomavirus (strain P16 small-plaque)

Seq: 384 a.a.

Struc: 285 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/16.16.5139

EMBO J 16:5139-5148 (1997)

PubMed id: 9305654

High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding.

T.Stehle, S.C.Harrison.

ABSTRACT

The crystal structure of a recombinant polyomavirus VP1 pentamer (residues 32-320) in complex with a branched disialylated hexasaccharide receptor fragment has been determined at 1.9 A resolution. The result extends our understanding of oligosaccharide receptor recognition. It also suggests a mechanism for enhancing the fidelity of virus assembly. We have previously described the structure of the complete polyomavirus particle complexed with this receptor fragment at 3.65 A. The model presented here offers a much more refined view of the interactions that determine carbohydrate recognition and allows us to assign additional specific contacts, in particular those involving the (alpha2,6)-linked, branching sialic acid. The structure of the unliganded VP1 pentamer, determined independently, shows that the oligosaccharide fits into a preformed groove and induces no measurable structural rearrangements. A comparison with assembled VP1 in the virus capsid reveals a rearrangement of residues 32-45 at the base of the pentamer. This segment may help prevent the formation of incorrectly assembled particles by reducing the likelihood that the C-terminal arm will fold back into its pentamer of origin.

Selected figure(s)

Figure 2.
Figure 2 Difference Fourier electron density, in stereo, for the oligosaccharide, calculated at 2.0 Å resolution and contoured at 2.5 . Figure prepared with O (Jones et al., 1991).

Figure 3.
Figure 3 The carbohydrate binding site of VP1. (A) Schematic view of the interactions. Hydrogen bonds are represented by thin broken lines, and hydrophobic contacts are shown as thick gray broken lines. Asp85#, located at the tip of the BC2-loop of the clockwise VP1 neighbor, approaches the N-acetyl group of NeuNAc-1. The small circles labeled 'W' represent water molecules. (B) Top view of the binding surface of VP1, showing the groove that accommodates NeuNAc-1–( 2,3)–Gal and the shallow pocket for NeuNAc-2. The yellow arrow indicates the attachment site for additional sugars. The surface has been calculated with MS (Connolly, 1983) using a probe radius of 1.4 Å. (C) View into the carbohydrate binding site, showing the interactions with the NeuNAc-1–( 2,3)–Gal moiety. (D) Interactions as in (C), with the viewpoint rotated by 90°, so that we are looking along the oligosaccharide chain from its sialic-acid end. (E) Interactions with NeuNAc-2. In panels (C–E), residues that form hydrogen bonds with the carbohydrate are colored orange and residues that form hydrophobic contacts, magenta. Residues that do not directly contact the carbohydrate are shown in gray. Water molecules are represented with green spheres and hydrogen bonds are shown as broken lines. Figure prepared with RIBBONS (Carson, 1987) (panels A, C, D and E) and O (Jones et al., 1991) (panel B).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 5139-5148) copyright 1997.

Figures were selected by an automated process.