5YTX

Crystal structure of YB1 cold-shock domain in complex with UCAACU

Summary for 5YTX

• Entry DOI: 10.2210/pdb5ytx/pdb
• Related: 5YTS 5YTT 5YTV
• Descriptor: Nuclease-sensitive element-binding protein 1, RNA (5'-R(P*UP*CP*AP*AP*CP*U)-3') (3 entities in total)
• Functional Keywords: yb1, cold-shock domain, caac, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 10833.17

Authors

Yang, X.,Huang, Y. (deposition date: 2017-11-20, release date: 2018-12-05, Last modification date: 2023-11-22)

Primary citation

Yang, X.J.,Zhu, H.,Mu, S.R.,Wei, W.J.,Yuan, X.,Wang, M.,Liu, Y.,Hui, J.,Huang, Y.
Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA.
J.Biol.Chem., 294:10998-11010, 2019

PubMed Abstract: The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1-mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunoprecipitation coupled RNA-Seq (iCLIP-Seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of a variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1-RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 Å resolution. The structure revealed that CSD interacts with RNA mainly through π-π stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA-binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD-RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.

PubMed: 31160337
DOI: 10.1074/jbc.RA119.007545

Experimental method

X-RAY DIFFRACTION (1.551 Å)