8YTO

Single-chain Fv antibody of E11 complex with NP-glycine

This is a non-PDB format compatible entry.

Summary for 8YTO

• Entry DOI: 10.2210/pdb8yto/pdb
• Descriptor: Single-chain Fv antibody of E11, 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, GLYCEROL, ... (5 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: 26925.84

Authors

Yoshida, M.,Hanazono, Y.,Numoto, N.,Ito, N.,Oda, M. (deposition date: 2024-03-26, release date: 2024-07-03, Last modification date: 2024-10-16)

Primary citation

Yoshida, M.,Hanazono, Y.,Numoto, N.,Nagao, S.,Yabuno, S.,Kitagawa, Y.,Sekiguchi, H.,Ito, N.,Azuma, T.,Oda, M.
Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758:110068-110068, 2024

PubMed Abstract: Affinity maturation increases antigen-binding affinity and specificity of antibodies by somatic hypermutation. Various monoclonal antibodies against (4-hydroxy-3-nitrophenyl)acetyl (NP) were obtained during affinity maturation. Among them, highly matured anti-NP antibodies, such as E11 and E3, possess Cys96 and Cys100 in the complementarity-determining region 3 of the heavy chain, which would form a disulfide bond. In this study, we evaluated the effects of disulfide bonds on antigen binding by generating single-chain Fv (scFv) antibodies of E11 and its mutants, E11_C96K/C100E and E11_C96K/C100Q, and determined their antigen-binding thermodynamics and kinetics. The binding affinities of the Cys mutants were lower than that of E11 scFv, indicating that the disulfide bond contributed to antigen binding, especially for stable complex formation. This was also supported by the decreased affinity of E11 scFv in the presence of a reducing agent. The crystal structures of NP-free and NP-bound E11 scFvs were determined at high resolution, showing the existence of a disulfide bond between Cys96 and Cys100, and the antigen recognition mechanism, which could be compared with those of other anti-NP antibodies, such as germline-type N1G9 and matured-type C6, as reported previously. These structures could explain the molecular basis of changes in antigen-binding affinity and thermal stability in the absence or presence of antigens. Small-angle X-ray scattering further showed a local conformational change in E11 scFv upon antigen binding in solution.

PubMed: 38909835
DOI: 10.1016/j.abb.2024.110068

Experimental method

X-RAY DIFFRACTION (1.04 Å)