6KUG

Crystal structure of YBX1 CSD with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs.

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.

(2020) Proc.Natl.Acad.Sci.USA --: --

  • DOI: 10.1073/pnas.1910862117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 5-Methylcytosine (m <sup>5 </sup>C) 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 m <sup>5 </sup>C RNA modification influences ad ...

    5-Methylcytosine (m 5 C) 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 m 5 C 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 Drosophila ovary by preferentially binding to m 5 C-containing RNAs. YPS is genetically demonstrated to function intrinsically for GSC maintenance, proliferation, and progeny differentiation in the Drosophila 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 m 5 C RNA in vitro. Moreover, YPS also preferentially binds to m 5 C-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 m 5 C binding. Overexpression of RNA-binding-defective YPS and YBX1 proteins disrupts GSC development. Taken together, our findings show that m 5 C RNA modification plays an important role in adult stem cell development.


    Organizational Affiliation

    Stowers Institute for Medical Research, Kansas City, MO 64110; liss6@sustc.edu.cn tgx@stowers.org.,National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602 Shanghai, China.,Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS 66160.,Department of Biology, Southern University of Science and Technology of China, 518055 Guangdong, China.,Harbin Institute of Technology, 150001 Heilongjiang, China.,Stowers Institute for Medical Research, Kansas City, MO 64110.,Department of Biology, Southern University of Science and Technology of China, 518055 Guangdong, China; liss6@sustc.edu.cn tgx@stowers.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclease-sensitive element-binding protein 1
A
79Homo sapiensMutation(s): 0 
Gene Names: YBX1 (NSEP1, YB1)
Find proteins for P67809 (Homo sapiens)
Go to Gene View: YBX1
Go to UniProtKB:  P67809
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*CP*CP*U)-3')B4Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 66.473α = 90.00
b = 66.473β = 90.00
c = 34.438γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-09-02 
  • Released Date: 2020-02-05 
  • Deposition Author(s): Zou, F., Li, S.

Revision History 

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-19
    Type: Database references