5YTV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 

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:  

  • 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 (miRNA) 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 crosslinking 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

    Chinese Academy of Sciences, China.,Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclease-sensitive element-binding protein 1
A
83Homo 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*UP*CP*AP*UP*CP*U)-3')B6synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 66.275α = 90.00
b = 66.275β = 90.00
c = 35.195γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2019-07-24
    Type: Data collection, Database references