Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content

• Total Structure Weight: 10.81 kDa 
• Atom Count: 717 
• Modelled Residue Count: 79 
• Deposited Residue Count: 89 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

5YTV

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

• PDB DOI: 10.2210/pdb5YTV/pdb
• NDB: 5YTV

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-20 Released: 2018-12-05 
• Deposition Author(s): Yang, X., Huang, Y.
• Funding Organization(s): National Natural Science Foundation of China, Strategic Priority Research Program of the Chinese Academy of Sciences

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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 

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

• PubMed: 31160337 
• DOI: 10.1074/jbc.RA119.007545
• Primary Citation of Related Structures:  
  5YTS, 5YTT, 5YTV, 5YTX


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease-sensitive element-binding protein 1	A	83	Homo sapiens	Mutation(s): 0  Gene Names: YBX1, NSEP1, YB1
UniProt & NIH Common Fund Data Resources
Find proteins for P67809 (Homo sapiens) Explore P67809  Go to UniProtKB:  P67809
PHAROS:  P67809 GTEx:  ENSG00000065978

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*CP*AP*UP*CP*U)-3')	B	6	synthetic 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 = 66.275	α = 90
b = 66.275	β = 90
c = 35.195	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91640102
Strategic Priority Research Program of the Chinese Academy of Sciences	China	XDB08010202

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