SNAP output for PDB entry 7tqb [SNAP web server]

PDB-id

7tqb; SNAP-derived features in text and JSON formats; DNAproDB

Class

immune system-DNA-RNA hybrid

Method

X-ray (3.1 Å)

Summary

Crystal structure of monoclonal s9.6 fab bound to DNA-RNA hybrid

Reference

Bou-Nader C, Bothra A, Garboczi DN, Leppla SH, Zhang J (2022): "Structural basis of R-loop recognition by the S9.6 monoclonal antibody." Nat Commun, 13, 1641. doi: 10.1038/s41467-022-29187-7.

Abstract

R-loops are ubiquitous, dynamic nucleic-acid structures that play fundamental roles in DNA replication and repair, chromatin and transcription regulation, as well as telomere maintenance. The DNA-RNA hybrid-specific S9.6 monoclonal antibody is widely used to map R-loops. Here, we report crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. We demonstrate that S9.6 exhibits robust selectivity in binding hybrids over double-stranded (ds) RNA and in categorically rejecting dsDNA. S9.6 asymmetrically recognizes a compact epitope of two consecutive RNA nucleotides via their 2'-hydroxyl groups and six consecutive DNA nucleotides via their backbone phosphate and deoxyribose groups. Recognition is mediated principally by aromatic and basic residues of the S9.6 heavy chain, which closely track the curvature of the hybrid minor groove. These findings reveal the molecular basis for S9.6 recognition of R-loops, detail its binding specificity, identify a new hybrid-recognition strategy, and provide a framework for S9.6 protein engineering.