6L6L

Structural basis of NR4A2 homodimers binding to selective Nur-responsive elements


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis of binding of homodimers of the nuclear receptor NR4A2 to selective Nur-responsive DNA elements.

Jiang, L.Dai, S.Li, J.Liang, X.Qu, L.Chen, X.Guo, M.Chen, Z.Chen, L.Wei, H.Chen, Y.

(2019) J Biol Chem 294: 19795-19803

  • DOI: https://doi.org/10.1074/jbc.RA119.010730
  • Primary Citation of Related Structures:  
    6L6L, 6L6Q

  • PubMed Abstract: 

    Proteins of nuclear receptor subfamily 4 group A (NR4A), including NR4A1/NGFI-B, NR4A2/Nurr1, and NR4A3/NOR-1, are nuclear transcription factors that play important roles in metabolism, apoptosis, and proliferation. NR4A proteins recognize DNA response elements as monomers or dimers to regulate the transcription of a variety of genes involved in multiple biological processes. In this study, we determined two crystal structures of the NR4A2 DNA-binding domain (NR4A2-DBD) bound to two Nur-responsive elements: an inverted repeat and an everted repeat at 2.6-2.8 Å resolution. The structures revealed that two NR4A2-DBD molecules bind independently to the everted repeat, whereas two other NR4A2-DBD molecules form a novel dimer interface on the inverted repeat. Moreover, substitution of the interfacial residue valine 298 to lysine as well as mutation of DNA bases involved in the interactions abolished the dimerization. Overall, our structural, biochemical, and bioinformatics analyses provide a molecular basis for the binding of the NR4A2 protein dimers to NurREs and advance our understanding of the dimerization specificity of nuclear receptors.


  • Organizational Affiliation

    Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor related 1
A, B
85Homo 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(*AP*AP*AP*GP*GP*TP*CP*AP*AP*AP*CP*TP*GP*TP*GP*AP*CP*CP*TP*AP*T)-3')21Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*TP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*TP*TP*GP*AP*CP*CP*TP*T)-3')21Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.405α = 90
b = 64.315β = 96.84
c = 60.776γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81372904 and 81570537
National Natural Science Foundation of ChinaChina81272971

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description