6KUG

Crystal structure of YBX1 CSD with RNA

Summary for 6KUG

• Entry DOI: 10.2210/pdb6kug/pdb
• Descriptor: Nuclease-sensitive element-binding protein 1, RNA (5'-R(P*GP*CP*CP*U)-3') (3 entities in total)
• Functional Keywords: csd, 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: 9927.56

Authors

Zou, F.,Li, S. (deposition date: 2019-09-02, release date: 2020-02-05, Last modification date: 2024-03-27)

Primary citation

Zou, F.,Tu, R.,Duan, B.,Yang, Z.,Ping, Z.,Song, X.,Chen, S.,Price, A.,Li, H.,Scott, A.,Perera, A.,Li, S.,Xie, T.
DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs.
Proc.Natl.Acad.Sci.USA, 117:3603-3609, 2020

PubMed Abstract: 5-Methylcytosine (mC) is a RNA modification that exists in tRNAs and rRNAs and was recently found in mRNAs. Although it has been suggested to regulate diverse biological functions, whether mC RNA modification influences adult stem cell development remains undetermined. In this study, we show that Ypsilon schachtel (YPS), a homolog of human Y box binding protein 1 (YBX1), promotes germ line stem cell (GSC) maintenance, proliferation, and differentiation in the ovary by preferentially binding to mC-containing RNAs. YPS is genetically demonstrated to function intrinsically for GSC maintenance, proliferation, and progeny differentiation in the ovary, and human YBX1 can functionally replace YPS to support normal GSC development. Highly conserved cold-shock domains (CSDs) of YPS and YBX1 preferentially bind to mC RNA in vitro. Moreover, YPS also preferentially binds to mC-containing RNAs, including mRNAs, in germ cells. The crystal structure of the YBX1 CSD-RNA complex reveals that both hydrophobic stacking and hydrogen bonds are critical for mC binding. Overexpression of RNA-binding-defective YPS and YBX1 proteins disrupts GSC development. Taken together, our findings show that mC RNA modification plays an important role in adult stem cell development.

PubMed: 32015133
DOI: 10.1073/pnas.1910862117

Experimental method

X-RAY DIFFRACTION (1.4 Å)