SNAP annotations: PDB entry 7yex

PDB-id

7yex; DSSR-derived features in text and JSON formats; DNAproDB

Class

RNA binding protein-RNA

Method

X-ray (2.0 Å)

Summary

Structure of mmigf2bp3 in complex with 8-mer RNA

Reference

Li X, Guo W, Wen Y, Meng C, Zhang Q, Chen H, Zhao X, Wu B (2025): "Structural basis for the RNA binding properties of mouse IGF2BP3." Structure. doi: 10.1016/j.str.2025.01.022.

Abstract

IGF2BP family proteins (IGF2BPs) contain six tandem RNA-binding domains (RBDs), resulting in highly complex RNA binding properties. Dissecting how IGF2BPs recognize their RNA targets is essential for understanding their regulatory roles in gene expression. Here, we have determined the crystal structures of mouse IGF2BP3 constructs complexed with different RNA substrates. Our structures reveal that the IGF2BP3-RRM12 domains can recognize CA-rich elements up to 5-nt in length, mainly through RRM1. We also captured the antiparallel RNA-binding mode of the IGF2BP3-KH12 domains, with five nucleotides bound by KH1 and two nucleotides bound by KH2. Furthermore, our structural and biochemical studies suggest that the IGF2BP3-KH12 domains could recognize the "zipcode" RNA element within the β-actin mRNA. Finally, we analyzed the similarities and differences of the RNA-binding properties between the KH12 and KH34. Our studies provide structural insights into RNA target recognition by mouse IGF2BP3.