6A6J

Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay.

Yang, Y.Wang, L.Han, X.Yang, W.L.Zhang, M.Ma, H.L.Sun, B.F.Li, A.Xia, J.Chen, J.Heng, J.Wu, B.Chen, Y.S.Xu, J.W.Yang, X.Yao, H.Sun, J.Lyu, C.Wang, H.L.Huang, Y.Sun, Y.P.Zhao, Y.L.Meng, A.Ma, J.Liu, F.Yang, Y.G.

(2019) Mol Cell 75: 1188-1202.e11

  • DOI: https://doi.org/10.1016/j.molcel.2019.06.033
  • Primary Citation of Related Structures:  
    6A6J

  • PubMed Abstract: 

    The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the maternal environment is converted to an environment of embryonic-driven development through dramatic reprogramming. However, how maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m 5 C) modification in zebrafish early embryos, we found that m 5 C-modified maternal mRNAs display higher stability than non-m 5 C-modified mRNAs during MZT. We discovered that Y-box binding protein 1 (Ybx1) preferentially recognizes m 5 C-modified mRNAs through π-π interactions with a key residue, Trp45, in Ybx1's cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Together with the mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m 5 C-dependent manner. Our study demonstrates an unexpected mechanism of RNA m 5 C-regulated maternal mRNA stabilization during zebrafish MZT, highlighting the critical role of m 5 C mRNA modification in early development.


  • Organizational Affiliation

    CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zebra fish Y-box protein1 (YB-1)
A, C
93Danio rerioMutation(s): 0 
Gene Names: ybx1
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
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')
B, D
6Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.201α = 90
b = 60.866β = 118.97
c = 56.513γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.4: 2019-10-02
    Changes: Data collection, Database references