8HYL

Crystal structure of DO1 Fv-clasp fragment

Summary for 8HYL

• Entry DOI: 10.2210/pdb8hyl/pdb
• Descriptor: VH-SARAH, VL-SARAH (3 entities in total)
• Functional Keywords: antibody, immune system
• Biological source: Mus musculus; More
• Total number of polymer chains: 4
• Total formula weight: 75764.03

Authors

Anan, Y.,Lu, P.,Nagata, K.,Itakura, M.,Uchida, K. (deposition date: 2023-01-06, release date: 2024-02-14, Last modification date: 2024-10-30)

Primary citation

Anan, Y.,Itakura, M.,Shimoda, T.,Yamaguchi, K.,Lu, P.,Nagata, K.,Dong, J.,Ueda, H.,Uchida, K.
Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins.
Commun Biol, 7:149-149, 2024

PubMed Abstract: Anti-DNA antibodies (Abs), serological hallmarks of systemic lupus erythematosus (SLE) and markers for diagnosis and disease activity, show a specificity for non-nucleic acid molecules, such as N-pyrrolated proteins (pyrP) containing N-pyrrole-L-lysine (pyrK) residues. However, the detailed mechanism for the binding of anti-DNA Abs to pyrP remains unknown. In the present study, to gain structural insights into the dual-specificity of anti-DNA Abs, we used phage display to obtain DNA-binding, single-chain variable fragments (scFvs) from SLE-prone mice and found that they also cross-reacted with pyrP. It was revealed that a variable heavy chain (VH) domain is sufficient for the recognition of DNA/pyrP. Identification of an antigenic sequence containing pyrK in pyrP suggested that the presence of both pyrK and multiple acidic amino acid residues plays important roles in the electrostatic interactions with the Abs. X-ray crystallography and computer-predicted simulations of the pyrK-containing peptide-scFv complexes identified key residues of Abs involved in the interaction with the antigens. These data provide a mechanistic insight into the molecular basis of the dual-specificity of the anti-DNA Abs and provide a basis for therapeutic intervention against SLE.

PubMed: 38310133
DOI: 10.1038/s42003-024-05851-0

Experimental method

X-RAY DIFFRACTION (2 Å)