9JZT | pdb_00009jzt

Crystal structure of ZBTB20 in complex with mouse AFP promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: in silico
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Literature

Structural insights into ZBTB20 action at the AFP promoter.

Yang, L.Xie, H.Wan, X.Li, M.Lv, M.Duan, Y.Shi, Y.Zhang, W.J.Li, F.

(2025) Structure 33: 1398-1407.e2

  • DOI: https://doi.org/10.1016/j.str.2025.05.009
  • Primary Citation of Related Structures:  
    9JZT

  • PubMed Abstract: 

    ZBTB20, a C2H2 zinc finger and broad-complex, tramtrack and bric-à-brac (BTB) domain-containing protein, is crucial for organ development and metabolic homeostasis. Its functionality is dependent on its DNA-binding zinc fingers, and heterozygous mutations within these regions are linked to Primrose syndrome, which is characterized by various physical and developmental abnormalities. However, the molecular basis underlying ZBTB20 zinc finger recognition of DNA remains largely unknown. Here, we present the crystal structure of ZBTB20 zinc fingers 1-4 (ZF1-4) in complex with the mouse alpha-fetoprotein (AFP) promoter in the region spanning positions -104 to -90. In combination with calorimetric analysis, we established that ZF1-3 is essential for the recognition of the AFP promoter and identified key residues involved in DNA binding. Furthermore, our data allow us to correlate Primrose syndrome mutations with alterations in DNA-binding efficacy. Overall, our study provides mechanistic insights into the physiological and pathological roles of ZBTB20 zinc fingers.


  • Organizational Affiliation
    • MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China. Electronic address: ylna@ustc.edu.cn.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger and BTB domain-containing protein 20118Homo sapiensMutation(s): 0 
Gene Names: ZBTB20DPZFZNF288
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC78 (Homo sapiens)
Explore Q9HC78 
Go to UniProtKB:  Q9HC78
PHAROS:  Q9HC78
GTEx:  ENSG00000181722 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HC78
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*TP*CP*CP*TP*TP*AP*CP*GP*TP*TP*GP*AP*AP*G)-3')16Mus musculus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*TP*CP*AP*AP*CP*GP*TP*AP*AP*GP*GP*AP*A)-3')16Mus musculus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.944α = 90
b = 103.944β = 90
c = 77.216γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371282

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release