5YTV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA.

Yang, X.J.Zhu, H.Mu, S.R.Wei, W.J.Yuan, X.Wang, M.Liu, Y.Hui, J.Huang, Y.

(2019) J Biol Chem 294: 10998-11010

  • DOI: 10.1074/jbc.RA119.007545
  • Primary Citation of Related Structures:  
    5YTX, 5YTS, 5YTT, 5YTV

  • 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 ...

    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 CD44 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.


    Organizational Affiliation

    the Shanghai Key Laboratory of Molecular Andrology, Shanghai 200031, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclease-sensitive element-binding protein 1A83Homo sapiensMutation(s): 0 
Gene Names: YBX1NSEP1YB1
Find proteins for P67809 (Homo sapiens)
Explore P67809 
Go to UniProtKB:  P67809
NIH Common Fund Data Resources
PHAROS  P67809
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*UP*CP*AP*UP*CP*U)-3')B6synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.70 Å
    • R-Value Free: 0.228 
    • R-Value Work: 0.196 
    • R-Value Observed: 0.199 
    • Space Group: P 62
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 66.275α = 90
    b = 66.275β = 90
    c = 35.195γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2017-11-20 
    • Released Date: 2018-12-05 
    • Deposition Author(s): Yang, X., Huang, Y.

    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of ChinaChina91640102
    Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08010202

    Revision History 

    • Version 1.0: 2018-12-05
      Type: Initial release
    • Version 1.1: 2019-06-19
      Changes: Data collection, Database references
    • Version 1.2: 2019-07-24
      Changes: Data collection, Database references