9SZP

Crystal structure of the human YTHDC2 YTH domain in complex with m6A DNA

Summary for 9SZP

• Entry DOI: 10.2210/pdb9szp/pdb
• Descriptor: 3'-5' RNA helicase YTHDC2, DNA (5'-D(*GP*GP*(6MA)P*CP*TP*A)-3') (3 entities in total)
• Functional Keywords: ythdc2, dna, m6a, rna binding protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 20531.24

Authors

Bedi, R.K.,Caflisch, A. (deposition date: 2025-10-15, release date: 2026-04-01)

Primary citation

Bedi, R.K.,Caflisch, A.
A DNA-Based Binding Assay for the m 6 A-RNA Reader Proteins.
Chembiochem, 27:e202500897-e202500897, 2026

PubMed Abstract: N6-methyladenosine (mA) is the most prevalent internal modification in eukaryotic messenger RNA. Dysregulation of mA-RNA signaling has been implicated in a wide range of human diseases. The N6-methyladenosine modifications in DNA (6mA) is much rarer, and its role is still debated. Here, we report the first holo crystal structure of the mA-RNA reader YTHDC2. The 1.6 Å resolution structure of YTHDC2 bound to the single-strand (ss) hexanucleotide GG(6mA)CTA-DNA shows an essentially identical binding mode of (6mA)CT-DNA as (mA)CU-RNA in the other four human reader proteins YTHDC1 and YTHDF1-3. Comparative analysis of the binding of fluorescent-labeled 6mA-ssDNA and mA-RNA revealed that the five human mA-RNA readers exhibit slightly stronger binding affinity for 6mA-modified DNA with a factor ranging from about 1.3 for YTHDC1 to 30 for YTHDC2. Given the similar affinity and the similar binding mode of 6mA-ssDNA and mA-RNA, we set up to develop a fluorescence polarization (FP) binding assay that uses a fluorescent-labeled 6mA-containing ssDNA as probe. The DNA-based FP assay shows high stability and robustness, making it suitable for high-throughput screening applications. The assay provides a powerful and cost-efficient platform to accelerate the discovery of small-molecule modulators targeting mA-RNA reader proteins.

PubMed: 41863816
DOI: 10.1002/cbic.202500897

Experimental method

X-RAY DIFFRACTION (1.58 Å)