2R04

STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES

Replaces:  1R04

Summary for 2R04

• Entry DOI: 10.2210/pdb2r04/pdb
• Related: 1R08 1R09 2R06 2R07 2RM2 2RR1 2RS1 2RS3 2RS5
• Descriptor: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1), HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2), HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3), ... (6 entities in total)
• Functional Keywords: rhinovirus coat protein, icosahedral virus, virus
• Biological source: Human rhinovirus 14; More
• Cellular location: Protein VP2: Virion. Protein VP3: Virion. Protein VP1: Virion. Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3B: Virion (Potential). Picornain 3C: Host cytoplasm (Potential). RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential): P03303 P03303 P03303 P03303
• Total number of polymer chains: 4
• Total formula weight: 94824.96

Authors

Badger, J.,Smith, T.J.,Rossmann, M.G. (deposition date: 1988-10-03, release date: 1990-01-15, Last modification date: 2024-05-22)

Primary citation

Badger, J.,Minor, I.,Oliveira, M.A.,Smith, T.J.,Rossmann, M.G.
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.
Proteins, 6:1-19, 1989

PubMed Abstract: X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.

PubMed: 2558377
DOI: 10.1002/prot.340060102

Experimental method

X-RAY DIFFRACTION (3 Å)