9JKO | pdb_00009jko

Crystal structure of the RNA- binding domain of human ZAR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

Molecular insights into RNA recognition by the ZAR1 C-terminal domain.

Liu, Q.Ma, H.He, X.Xu, C.Zhang, J.

(2025) FEBS Lett 

  • DOI: https://doi.org/10.1002/1873-3468.70080
  • Primary Citation of Related Structures:  
    9JKO

  • PubMed Abstract: 

    Zygote arrested-1 (ZAR1)-dependent translational repression plays an important role during early oogenesis. Here, we solved the crystal structure of the C-terminal domain of ZAR1, which contains three zinc-binding motifs, and confirmed its ability to bind to RNAs derived from translation control sequence elements within the 3'-UTRs of Wee1 and Mos mRNAs. By using the AlphaFold server, we obtained a predicted model for the structure of the ZAR1 C-terminal domain bound with a 13-nt RNA. Mutagenesis and biochemistry experiments further validated the ZAR1-RNA interaction. Therefore, our study provides insights into RNA recognition by the ZAR1 zinc-binding domain and the role of ZAR1 in repressing gene expression. Impact statement Zygote arrested-1 (ZAR1)-dependent translational repression finely orchestrates gene expression during early oogenesis. Here, we solved the high-resolution structure of the C-terminal zinc-binding domain of ZAR1 and confirmed its binding to RNA. The modeled ZAR1-RNA complex by Alphafold further provides insight into RNA recognition by ZAR1.


  • Organizational Affiliation
    • Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zygote arrest protein 1
A, B
98Homo sapiensMutation(s): 0 
Gene Names: ZAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86SH2 (Homo sapiens)
Explore Q86SH2 
Go to UniProtKB:  Q86SH2
GTEx:  ENSG00000182223 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86SH2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.61α = 90
b = 58.45β = 90
c = 81.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release