6A6J

Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA

Summary for 6A6J

• Entry DOI: 10.2210/pdb6a6j/pdb
• Descriptor: Zebra fish Y-box protein1 (YB-1), RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3'), ZINC ION, ... (4 entities in total)
• Functional Keywords: ob-fold, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Danio rerio (Zebrafish); More
• Total number of polymer chains: 4
• Total formula weight: 24039.73

Authors

Zhang, M.M.,Wu, B.X.,Huang, Y.,Ma, J.B. (deposition date: 2018-06-28, release date: 2019-06-19, Last modification date: 2024-03-27)

Primary citation

Yang, Y.,Wang, L.,Han, X.,Yang, W.L.,Zhang, M.,Ma, H.L.,Sun, B.F.,Li, A.,Xia, J.,Chen, J.,Heng, J.,Wu, B.,Chen, Y.S.,Xu, J.W.,Yang, X.,Yao, H.,Sun, J.,Lyu, C.,Wang, H.L.,Huang, Y.,Sun, Y.P.,Zhao, Y.L.,Meng, A.,Ma, J.,Liu, F.,Yang, Y.G.
RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay.
Mol.Cell, 75:1188-1202.e11, 2019

PubMed Abstract: The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the maternal environment is converted to an environment of embryonic-driven development through dramatic reprogramming. However, how maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (mC) modification in zebrafish early embryos, we found that mC-modified maternal mRNAs display higher stability than non-mC-modified mRNAs during MZT. We discovered that Y-box binding protein 1 (Ybx1) preferentially recognizes mC-modified mRNAs through π-π interactions with a key residue, Trp45, in Ybx1's cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Together with the mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an mC-dependent manner. Our study demonstrates an unexpected mechanism of RNA mC-regulated maternal mRNA stabilization during zebrafish MZT, highlighting the critical role of mC mRNA modification in early development.

PubMed: 31399345
DOI: 10.1016/j.molcel.2019.06.033

Experimental method

X-RAY DIFFRACTION (2.255 Å)