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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Bioinformatic and experimental characterization of the RBM15 RNA binding protein.

Emma Bose1, Caleb Mayes1, Lance Ellis1

  • 1Department of Chemistry, New York University, New York, New York, USA.

Journal of Structural Biology
|November 26, 2025
PubMed
Summary
This summary is machine-generated.

The RNA binding motif 15 protein (RBM15) uses its RNA recognition motifs (RRMs) to bind structured RNAs. This study reveals how RBM15

Keywords:
AlphaFoldFIRREProtein-RNA interactionRBM15RRMsXISTcatRAPIDlncRNA

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Genetics

Background:

  • The RNA binding motif 15 protein (RBM15) is crucial for cellular processes like gene silencing and hematopoiesis.
  • While the SPOC domain of RBM15 mediates protein-protein interactions, the RNA-binding mechanism of its N-terminal RNA recognition motifs (RRMs) is not fully understood.

Purpose of the Study:

  • To elucidate the structural mechanism by which RBM15's RRMs interact with RNA.
  • To identify specific RNA structures bound by RBM15.

Main Methods:

  • Bioinformatic analysis of public genome-wide RNA 2D structural probing and RNA binding protein (RBP) cross-linking and immunoprecipitation (CLIP) data.
  • In vitro binding assays.
  • Structural modeling and nuclear magnetic resonance (NMR) spectroscopy.

Main Results:

  • RBM15's RRMs cooperatively bind stem-loop RNA structures with high affinity (nanomolar).
  • RRMs 2 and 3 form a heterodimer through coaxial stacking.
  • This RRM heterodimer forms a sandwich-like structure around the bound RNA.

Conclusions:

  • The study reveals the structural basis of RBM15-RNA interaction, involving a heterodimer of RRMs 2 and 3.
  • This mechanism explains how RBM15 regulates biological functions through RNA binding.