Crystal structure of YBX1 CSD with m5C RNA

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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 U S A 117: 3603-3609

  • DOI: https://doi.org/10.1073/pnas.1910862117
  • Primary Citation of Related Structures:  
    6KTC, 6KUG

  • PubMed Abstract: 

    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

    Harbin Institute of Technology, 150001 Heilongjiang, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclease-sensitive element-binding protein 179Homo sapiensMutation(s): 0 
Gene Names: YBX1NSEP1YB1
UniProt & NIH Common Fund Data Resources
Find proteins for P67809 (Homo sapiens)
Explore P67809 
Go to UniProtKB:  P67809
PHAROS:  P67809
GTEx:  ENSG00000065978 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67809
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*(5MC)P*CP*U)-3')B [auth V]4Homo sapiens
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.706α = 90
b = 66.706β = 90
c = 34.224γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description