9UDP

Single-chain Fv antibody of B2

Summary for 9UDP

• Entry DOI: 10.2210/pdb9udp/pdb
• Descriptor: Single-chain Fv antibody of B2, FORMIC ACID, GLYCEROL, ... (4 entities in total)
• Functional Keywords: antigen binding, affinity maturation, somatic hypermutation, immune system
• Biological source: Mus musculus
• Total number of polymer chains: 1
• Total formula weight: 26217.90

Authors

Yoshida, M.,Hanazono, Y.,Numoto, N.,Ito, N.,Oda, M. (deposition date: 2025-04-07, release date: 2025-11-05, Last modification date: 2026-04-22)

Primary citation

Yoshida, M.,Hanazono, Y.,Numoto, N.,Yabuno, S.,Ito, N.,Azuma, T.,Oda, M.
Structural basis of affinity maturation of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies.
Arch.Biochem.Biophys., 775:110665-110665, 2026

PubMed Abstract: The phenomenon in which the antibody affinity for T cell-dependent antigens increases through multiple rounds of somatic hypermutation (SHM) is referred to as affinity maturation. The elucidation of the structural and physical properties of antibodies obtained at various stages of the affinity maturation process can help us understand the molecular recognition mechanism of proteins in general. For this purpose, we used anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) single-chain (scFv) antibodies, prepared from the parent antibodies F8, B2, C6, and E11, and analyzed the crystal structures either in the absence or presence of NP or (4-hydroxy-3,5-dinitrophenyl)acetyl (NNP). Comparison of the structures revealed that the antibodies shared a common antigen recognition architecture consisting of residues with basic side chains, Arg50 and Lys58/Arg58, in addition to those at the junctional positions of gene segments, Trp96 and Tyr95 or His100B. These residues are responsible for the recognition of antigenic determinants, nitro-, hydroxyl- and phenylacetyl-groups, through hydrogen bond formation. Second, the Trp33 to Leu33 mutation seemed to strengthen the interaction because the antigen was closer to the combining site. Finally, analysis of NP and NNP complexes showed little difference in the antigen recognition modes and in the overall structures of the complementarity-determining regions between C6 and E11 scFvs. It was suggested that the replacement of residues by SHM provided a unique binding site for each antibody by fine tuning the microenvironment without disturbing specificity.

PubMed: 41161463
DOI: 10.1016/j.abb.2025.110665

Experimental method

X-RAY DIFFRACTION (1.48 Å)