9VX3

Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp

Summary for 9VX3

• Entry DOI: 10.2210/pdb9vx3/pdb
• Descriptor: HisMab-1VH(S112C),Serine/threonine-protein kinase 4 18kDa subunit, HisMab-1VL,Serine/threonine-protein kinase 4 18kDa subunit, Polyhistidine peptide, ... (4 entities in total)
• Functional Keywords: hismab-1, fv-clasp, his-tag, immune system
• Biological source: Mus musculus; More
• Total number of polymer chains: 6
• Total formula weight: 78542.20

Authors

Hitomi, N.,Harada-Hikita, A.,Arimori, T. (deposition date: 2025-07-18, release date: 2025-12-17, Last modification date: 2025-12-24)

Primary citation

Hitomi, N.,Hoshi, S.,Kaneko, M.K.,Kato, R.,Iwasaki, K.,Takagi, J.,Kato, Y.,Harada-Hikita, A.,Arimori, T.
Functional and Structural Characterization of a Novel Anti-His-tag Antibody, HisMab-1.
J.Mol.Biol., 438:169574-169574, 2025

PubMed Abstract: The polyhistidine tag (His-tag) is one of the most widely used peptide tags for the purification of recombinant proteins, owing to its compatibility with immobilized metal affinity chromatography. While numerous anti-His-tag antibodies are commercially available, their quantitative affinity data and structural insights are limited. Here, we present a detailed physicochemical and structural characterization of a novel anti-His-tag antibody, HisMab-1. Isothermal titration calorimetry showed that the Fab fragment of HisMab-1 binds to a hexahistidine peptide in an enthalpy-driven manner, with a dissociation constant (K) of ∼30 nM at a neutral pH. The crystal structure of the HisMab-1-hexahistidine peptide complex at 2.39-Å resolution revealed that HisMab-1 primarily recognizes the first, second, fourth, and fifth histidine residues of the peptide through multiple interactions, including hydrogen bonding and π-π stacking, which collectively contribute to the high specificity of the antibody. Notably, HisMab-1 also binds to a His-tag embedded within a conformationally constrained β-hairpin loop without reducing affinity, highlighting its structural adaptability. These findings establish HisMab-1 as a high-affinity, high-specificity, structurally validated anti-His-tag antibody with broad potential in diverse protein engineering and structural biology applications.

PubMed: 41349762
DOI: 10.1016/j.jmb.2025.169574

Experimental method

X-RAY DIFFRACTION (2.39 Å)