1A3R

FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170)

Summary for 1A3R

• Entry DOI: 10.2210/pdb1a3r/pdb
• Descriptor: IGG2A 8F5 FAB (LIGHT CHAIN), IGG2A 8F5 FAB (HEAVY CHAIN), HUMAN RHINOVIRUS CAPSID PROTEIN VP2, ... (4 entities in total)
• Functional Keywords: immunoglobulin, antibody, rhinovirus, neutralization, continuous epitope, complex (immunoglobulin-viral peptide), viral protein-immune system complex, viral protein/immune system
• Biological source: Mus musculus (house mouse); More
• Cellular location: Capsid protein VP0: Virion . Capsid protein VP4: Virion . Capsid protein VP2: Virion . Capsid protein VP3: Virion . Capsid protein VP1: Virion . Protein 2B: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Protein 2C: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Protein 3A: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Protein 3AB: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Viral protein genome-linked: Virion . Protease 3C: Host cytoplasm . Protein 3CD: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . RNA-directed RNA polymerase: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side : P04936
• Total number of polymer chains: 3
• Total formula weight: 49716.09

Authors

Tormo, J.,Blaas, D.,Fita, I. (deposition date: 1998-01-23, release date: 1998-04-29, Last modification date: 2024-10-16)

Primary citation

Tormo, J.,Blaas, D.,Parry, N.R.,Rowlands, D.,Stuart, D.,Fita, I.
Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2.
EMBO J., 13:2247-2256, 1994

PubMed Abstract: The three-dimensional structure of the complex between the Fab fragment of an anti-human rhinovirus neutralizing antibody (8F5) and a cross-reactive synthetic peptide from the viral capsid protein VP2 has been determined at 2.5 A resolution by crystallographic methods. The refinement is presently at an R factor of 0.18 and the antigen-binding site and viral peptide are well defined. The peptide antigen adopts a compact fold by two tight turns and interacts through hydrogen bonds, some with ionic character, and van der Waals contacts with antibody residues from the six hypervariable loops as well as several framework amino acids. The conformation adopted by the peptide is closely related to the corresponding region of the viral protein VP2 on the surface of human rhinovirus 1A whose three-dimensional structure is known. Implications for the cross-reactivity between peptides and the viral capsid are discussed. The peptide-antibody interactions, together with the analysis of mutant viruses that escape neutralization by 8F5 suggest two different mechanisms for viral escape. The comparison between the complexed and uncomplexed antibody structures shows important conformational rearrangements, especially in the hypervariable loops of the heavy chain. Thus, it constitutes a clear example of the 'induced fit' molecular recognition mechanism.

PubMed: 8194515

Experimental method

X-RAY DIFFRACTION (2.1 Å)