Crystal structure of the Human TR4 DNA-Binding Domain with C-terminal extension (DBD-CTE) Homodimer Bound to DR1 Response Element

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 

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Structures of human TR4LBD-JAZF1 and TR4DBD-DNA complexes reveal the molecular basis of transcriptional regulation.

Liu, Y.Ma, L.Li, M.Tian, Z.Yang, M.Wu, X.Wang, X.Shang, G.Xie, M.Chen, Y.Liu, X.Jiang, L.Wu, W.Xu, C.Xia, L.Li, G.Dai, S.Chen, Z.

(2023) Nucleic Acids Res 51: 1443-1457

  • DOI: https://doi.org/10.1093/nar/gkac1259
  • Primary Citation of Related Structures:  
    7XV6, 7XV8, 7XV9, 7XVA

  • PubMed Abstract: 

    Testicular nuclear receptor 4 (TR4) modulates the transcriptional activation of genes and plays important roles in many diseases. The regulation of TR4 on target genes involves direct interactions with DNA molecules via the DNA-binding domain (DBD) and recruitment of coregulators by the ligand-binding domain (LBD). However, their regulatory mechanisms are unclear. Here, we report high-resolution crystal structures of TR4DBD, TR4DBD-DNA complexes and the TR4LBD-JAZF1 complex. For DNA recognition, multiple factors come into play, and a specific mutual selectivity between TR4 and target genes is found. The coactivators SRC-1 and CREBBP can bind at the interface of TR4 originally occupied by the TR4 activation function region 2 (AF-2); however, JAZF1 suppresses the binding through a novel mechanism. JAZF1 binds to an unidentified surface of TR4 and stabilizes an α13 helix never reported in the nuclear receptor family. Moreover, the cancer-associated mutations affect the interactions and the transcriptional activation of TR4 in vitro and in vivo, respectively. Overall, our results highlight the crucial role of DNA recognition and a novel mechanism of how JAZF1 reinforces the autorepressed conformation and influences the transcriptional activation of TR4, laying out important structural bases for drug design for a variety of diseases, including diabetes and cancers.

  • Organizational Affiliation

    State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NR2C2 proteinC [auth A],
D [auth B]
84Homo sapiensMutation(s): 0 
Gene Names: Nr2c2
UniProt & NIH Common Fund Data Resources
Find proteins for P49116 (Homo sapiens)
Explore P49116 
Go to UniProtKB:  P49116
PHAROS:  P49116
GTEx:  ENSG00000177463 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49116
Sequence Annotations
  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')A [auth C]18DNA molecule
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*CP*TP*GP*C)-3')B [auth D]18DNA molecule
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.146α = 90
b = 52.146β = 90
c = 242.701γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

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: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-03-08
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description