7TQB

Crystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid

Summary for 7TQB

• Entry DOI: 10.2210/pdb7tqb/pdb
• Descriptor: FAB S9.6 Heavy Chain, FAB S9.6 Light Chain, RNA, ... (6 entities in total)
• Functional Keywords: antibody fab dna:rna hybrid nucleic acid dna:rna hybrid binding protein, dna-rna hybrid, immune system-dna-rna hybrid complex, immune system/dna-rna hybrid
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 57284.80

Authors

Bou-Nader, C.,Zhang, J. (deposition date: 2022-01-26, release date: 2022-03-30, Last modification date: 2024-11-13)

Primary citation

Bou-Nader, C.,Bothra, A.,Garboczi, D.N.,Leppla, S.H.,Zhang, J.
Structural basis of R-loop recognition by the S9.6 monoclonal antibody.
Nat Commun, 13:1641-1641, 2022

PubMed 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.

PubMed: 35347133
DOI: 10.1038/s41467-022-29187-7

Experimental method

X-RAY DIFFRACTION (3.1 Å)