1NDG

Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme

Summary for 1NDG

• Entry DOI: 10.2210/pdb1ndg/pdb
• Related: 1DQJ 1DQM 1DQQ 1NBY 1NBZ 1NDG 1NDM
• Descriptor: antibody kappa light chain, immunoglobulin gamma 1 chain, Lysozyme C, ... (5 entities in total)
• Functional Keywords: antibody; lysozyme; mutant; hyhel-8, immune system-hydrolase complex, immune system/hydrolase
• Biological source: Mus musculus (house mouse); More
• Cellular location: Cell membrane; Single-pass membrane protein (Potential): P01865; Secreted: P00698
• Total number of polymer chains: 3
• Total formula weight: 60615.27

Authors

Mariuzza, R.A.,Li, Y.,Li, H.,Yang, F.,Smith-Gill, S.J. (deposition date: 2002-12-09, release date: 2003-06-03, Last modification date: 2024-10-16)

Primary citation

Li, Y.,Li, H.,Yang, F.,Smith-Gill, S.J.,Mariuzza, R.A.
X-ray snapshots of the maturation of an antibody response to a protein antigen
Nat.Struct.Biol., 10:482-488, 2003

PubMed Abstract: The process whereby the immune system generates antibodies of higher affinities during a response to antigen (affinity maturation) is a prototypical example of molecular evolution. Earlier studies have been confined to antibodies specific for small molecules (haptens) rather than for proteins. We compare the structures of four antibodies bound to the same site on hen egg white lysozyme (HEL) at different stages of affinity maturation. These X-ray snapshots reveal that binding is enhanced, not through the formation of additional hydrogen bonds or van der Waals contacts or by an increase in total buried surface, but by burial of increasing amounts of apolar surface at the expense of polar surface, accompanied by improved shape complementarity. The increase in hydrophobic interactions results from highly correlated rearrangements in antibody residues at the interface periphery, adjacent to the central energetic hot spot. This first visualization of the maturation of antibodies to protein provides insights into the evolution of high affinity in other protein-protein interfaces.

PubMed: 12740607
DOI: 10.1038/nsb930

Experimental method

X-RAY DIFFRACTION (1.9 Å)