PDBsum entry 1d3e

Virus/receptor

PDB id: 1d3e

Contents

Protein chains

185 a.a.*

285 a.a.*

252 a.a.*

238 a.a.*

29 a.a.*

* C-alpha coords only

References listed in PDB file

Key reference

Title

Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor.

Authors

P.R.Kolatkar, J.Bella, N.H.Olson, C.M.Bator, T.S.Baker, M.G.Rossmann.

Ref.

EMBO J, 1999, 18, 6249-6259. [DOI no: 10.1093/emboj/18.22.6249]

PubMed id

10562537

Abstract

Two human rhinovirus serotypes complexed with two- and five-domain soluble fragments of the cellular receptor, intercellular adhesion molecule-1, have been investigated by X-ray crystallographic analyses of the individual components and by cryo-electron microscopy of the complexes. The three-dimensional image reconstructions provide a molecular envelope within which the crystal structures of the viruses and the receptor fragments can be positioned with accuracy. The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes. Fitting of molecular models into the image reconstruction density identified the residues on the virus that interact with those on the receptor surface, demonstrating complementarity of the electrostatic patterns for the tip of the N-terminal receptor domain and the floor of the canyon. The complexes seen in the image reconstructions probably represent the first stage of a multistep binding process. A mechanism is proposed for the subsequent viral uncoating process.

Figure 5.
Figure 5 Roadmap representation (Chapman, 1993) showing the amino acids within the ICAM-1 footprint (thick outline) on the surface of (A) HRV16 and (B) HRV14. The figure shows one icosahedral asymmetric unit with a 5-fold axis at the top and 3-fold axes to the left and right at the bottom. Residues closer than 145 Å to the viral center, shaded in gray, outline the central and deepest region of the canyon.

Figure 6.
Figure 6 Stereo representations of electrostatic charge distribution in the canyon region of HRV16 (top), HRV14 (bottom) and the tip of ICAM-1. Charge distributions are represented by the usual colors. Residues that show charge complementarity are indicated and connected with dashed lines.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 6249-6259) copyright 1999.

Secondary reference #1

Title

The structure of the two amino-Terminal domains of human icam-1 suggests how it functions as a rhinovirus receptor and as an lfa-1 integrin ligand.

Authors

J.Bella, P.R.Kolatkar, C.W.Marlor, J.M.Greve, M.G.Rossmann.

Ref.

Proc Natl Acad Sci U S A, 1998, 95, 4140-4145. [DOI no: 10.1073/pnas.95.8.4140]

PubMed id

9539703

Figure 1.
Fig. 1. A diagram of an ICAM-1 molecule showing sites of glycosylation (lollipop-shaped structures) and the approximate location of binding sites of LFA-1, Mac-1, human rhinoviruses, fibrinogen, and Plasmodium falciparum-infected erythrocytes (PFIE).

Figure 5.
Fig. 5. Ribbon diagram showing docking of the I-domain of LFA-1 (green) with domain D1 of mutICAM-1 (orange). Coordination of the metal ion (purple) on the I-domain is completed by Glu-34 (white) on the -strand C of mutICAM-1. Additional residues of the I-domain (36) and of ICAM-1 (24) considered important for binding are shown in green and yellow, respectively.

Secondary reference #2

Title

The refined structure of human rhinovirus 16 at 2.15 a resolution: implications for the viral life cycle.

Authors

A.T.Hadfield, W.Lee, R.Zhao, M.A.Oliveira, I.Minor, R.R.Rueckert, M.G.Rossmann.

Ref.

Structure, 1997, 5, 427-441. [DOI no: 10.1016/S0969-2126(97)00199-8]

PubMed id

9083115

Figure 6.
Figure 6. A schematic diagram representing VP1 of HRV16, showing the binding site of the pocket factor (shown in ball-and-stick representation) and the WIN antiviral compounds (shown in pale blue). A cation on the fivefold axis is shown in yellow. The N termini of VP1, VP3 and VP4 also interact around the fivefold axis. One copy of each of VP1 and the N termini of VP3 and VP4 are shown as blue, red and green ribbon diagrams, respectively. The myristylated N terminus of VP4 is labelled (MYR). (The diagram was created using MOLSCRIPT [64].)

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

Structure of a human rhinovirus complexed with its receptor molecule.

Authors

N.H.Olson, P.R.Kolatkar, M.A.Oliveira, R.H.Cheng, J.M.Greve, A.Mcclelland, T.S.Baker, M.G.Rossmann.

Ref.

Proc Natl Acad Sci U S A, 1993, 90, 507-511. [DOI no: 10.1073/pnas.90.2.507]

PubMed id

8093643

Secondary reference #4

Title

A dimeric crystal structure for the n-Terminal two domains of intercellular adhesion molecule-1.

Authors

J.M.Casasnovas, T.Stehle, J.H.Liu, J.H.Wang, T.A.Springer.

Ref.

Proc Natl Acad Sci U S A, 1998, 95, 4134-4139. [DOI no: 10.1073/pnas.95.8.4134]

PubMed id

9539702

Figure 3.
Fig. 3. The dimer interface and ligand-binding residues. (A) Interacting residues in domain 1. Side chains are shown for residues that interact across the dimer interface in domain 1 (Fig. 2A). The conserved central Val-51 residue is blue, and Glu-34 is red. Salt bridges between residues at the periphery of the interface are dashed lines. (B) Stereoview (40) of the dimer. Side chains and carbons are shown for residues important in binding to LFA-1 (red and orange) (3, 37), human rhinoviruses 3, 14, 15, 36, and 41 (yellow and orange) (3-5), and P. falciparum (blue) (6). Only single amino acid substitutions that reduced binding 50% or 2 SD below control are shown.

Figure 4.
Fig. 4. A model for the ICAM-1 dimer on the cell surface. Domains 1 and 2 and their orientation in the dimer are from the crystal structure. The rod-like shape of domains 1-5 in the monomer and the bend between domains 3 and 4 are from electron microscopy (3, 36). Dimerization or proximity between domain 5 is based on hindrance of antibody binding to this domain in the dimer (25), and association at the transmembrane domain is based on its role in dimerization (24, 25).