6LC1

Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter.

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

(2020) Biochem Biophys Res Commun 523: 1-5

  • DOI: 10.1016/j.bbrc.2019.11.192
  • Primary Citation of Related Structures:  
    6LC1

  • PubMed Abstract: 
  • The nuclear receptor NR4A subfamily (NR4A1/NGFI-B, NR4A2/Nurr1 and NR4A3/NOR-1) can recognize different classes of DNA response elements either as a monomer, homodimer, or heterodimer. In this study, we determined the structure of the NR4A1 DNA-binding domain (NR4A1-DBD) bound to natural Nur-responsive elements (NurREs) in the promoter region of the pituitary proopiomelanocortin (POMC) gene (NurRE POMC ) at 3 ...

    The nuclear receptor NR4A subfamily (NR4A1/NGFI-B, NR4A2/Nurr1 and NR4A3/NOR-1) can recognize different classes of DNA response elements either as a monomer, homodimer, or heterodimer. In this study, we determined the structure of the NR4A1 DNA-binding domain (NR4A1-DBD) bound to natural Nur-responsive elements (NurREs) in the promoter region of the pituitary proopiomelanocortin (POMC) gene (NurRE POMC ) at 3.12 Å resolution. The NR4A1-DBD molecules bound independently to this element in our structure. The N-terminal helix H1 forms specific contacts with major groove, and C-terminal extension interact extensively with minor groove. Moreover our modelling structure of NR4A1 large fragment complexed with NurRE POMC indicated that ligand binding domain of NR4A might form dimer interactions to help recognize DNA. Overall, our analyses provide a molecular basis for DNA binding of NR4A proteins as a homodimer and novel insight into the molecular functions of NR4A modulation of gene expression.


    Organizational Affiliation

    Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China. Electronic address: yonghenc@163.com.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 4 group A member 1D [auth A], F [auth D], H [auth G], B [auth J]87Homo sapiensMutation(s): 0 
Gene Names: NR4A1GFRP1HMRNAK1
UniProt & NIH Common Fund Data Resources
Find proteins for P22736 (Homo sapiens)
Explore P22736 
Go to UniProtKB:  P22736
PHAROS:  P22736
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNAG [auth F], A [auth I]26Homo sapiens
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (25-MER)E [auth C], C [auth L]26Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.822α = 109.98
b = 63.21β = 90.21
c = 91.762γ = 89.54
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-11-16 
  • Released Date: 2019-12-18 
  • Deposition Author(s): Jiang, L., Chen, Y.

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: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-02-19
    Changes: Database references