7WNH

Crystal structure of Nurr1 binding to NBRE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Integrative analysis reveals structural basis for transcription activation of Nurr1 and Nurr1-RXR alpha heterodimer.

Zhao, M.Wang, N.Guo, Y.Li, J.Yin, Y.Dong, Y.Zhu, J.Peng, C.Xu, T.Liu, J.

(2022) Proc Natl Acad Sci U S A 119: e2206737119-e2206737119

  • DOI: https://doi.org/10.1073/pnas.2206737119
  • Primary Citation of Related Structures:  
    7WNH

  • PubMed Abstract: 

    Orphan nuclear receptor Nurr1 plays important roles in the progression of various diseases, including Parkinson's disease, neuroinflammation, Alzheimer's disease, and multiple sclerosis. It can recognize DNA as a monomer or heterodimer with retinoid X receptor α (RXRα). But the molecular mechanism of its transcriptional activity regulation is still largely unknown. Here we obtained a crystal structure of monomer Nurr1 (DNA- and ligand-binding domains, DBD and LBD) bound to NGFI-B response element. The structure exhibited two different forms with distinct DBD orientations, unveiling the conformational flexibility of nuclear receptor monomer. We then generated an integrative model of Nurr1-RXRα heterodimer. In the context of heterodimer, the structural flexibility of Nurr1 would contribute to its transcriptional activity modulation. We demonstrated that the DNA sequence may specifically modulate the transcriptional activity of Nurr1 in the absence of RXRα agonist, but the modulation can be superseded when the agonist binds to RXRα. Together, we propose a set of signaling pathways for the constitutive transcriptional activation of Nurr1 and provide molecular mechanisms for therapeutic discovery targeting Nurr1 and Nurr1-RXRα heterodimer.


  • Organizational Affiliation

    State Key Laboratory of Respiratory Disease, Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 4 group A member 2
A, B, C, D
350Homo sapiensMutation(s): 0 
Gene Names: NR4A2
UniProt & NIH Common Fund Data Resources
Find proteins for P43354 (Homo sapiens)
Explore P43354 
Go to UniProtKB:  P43354
PHAROS:  P43354
GTEx:  ENSG00000153234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43354
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')E,
H [auth I],
J [auth L],
L [auth O]
16synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')F,
G [auth H],
I [auth K],
K [auth N]
16synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.002α = 90
b = 124.002β = 90
c = 119.518γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Derived calculations
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description