9QLM

Solution structure of the TAF3-PHD bound to a H3K4me3Q5ser histone tail peptide with a serotonylated glutamine

Summary for 9QLM

• Entry DOI: 10.2210/pdb9qlm/pdb
• Related: 2k17
• NMR Information: BMRB: 34986
• Descriptor: Transcription initiation factor TFIID subunit 3, Histone H3.1, ZINC ION, ... (4 entities in total)
• Functional Keywords: serotonylation, methylation, histone h3, gene regulation, tfiid
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 2
• Total formula weight: 10270.52

Authors

van Ingen, H.,Gielingh, H.,Pulido-Cortes, L.,Thijssen, V.,Timmers, H.T.M.,Jongkees, S.,Honorato, R.V.,Bonvin, A.M.J.J.,Liu, M.,Yoshisada, R.,Soares, L.R. (deposition date: 2025-03-21, release date: 2025-05-14, Last modification date: 2025-07-23)

Primary citation

Pulido-Cortes, L.,Gielingh, H.,Thijssen, V.,Liu, M.,Yoshisada, R.,Romao Soares, L.,Nizamuddin, S.,Friedrich, F.,Greschik, H.,Peng, L.,Vargas Honorato, R.,Jung, M.,Bonvin, A.M.J.J.,Biniossek, M.L.,Schule, R.,Jongkees, S.,van Ingen, H.,Timmers, H.T.M.
Molecular determinants for recognition of serotonylated chromatin.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Post-translational modifications of histone tails constitute a key epigenetic mechanism controlling chromatin environment and gene transcription. Serotonylation of histone H3Q5 (H3Q5ser) is a recently discovered mark associated with active transcription of RNA polymerase II (pol II)-transcribed genes. The direct link between H3Q5ser and the pol II transcription machinery relies on the TFIID subunit TAF3. The presence of H3Q5ser enhances TAF3 binding to H3K4me3, but the molecular determinants underlying this interaction remained unclear. Here, we resolve the binding mode of TAF3-PHD to H3K4me3Q5ser identifying a novel binding surface for H3Q5ser using solution nuclear magnetic resonance spectroscopy. This reveals how H3Q5ser recognizes a conserved surface of the TAF3-PHD via CH-π interactions in an edge-face conformation involving a proline residue stabilized by a tryptophan. This combination of proline and tryptophan is unique to the PHD finger of TAF3 and conserved among TAF3 orthologues. Our findings establish a framework for the molecular recognition of serotonylated chromatin, laying the foundation for developing epigenetic inhibitors targeting serotonylation-dependent transcriptional regulation in neuronal development.

PubMed: 40637225
DOI: 10.1093/nar/gkaf612

Experimental method

SOLUTION NMR