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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.

(2019) Biochem.Biophys.Res.Commun. --: --

  • DOI: 10.1016/j.bbrc.2019.11.192

  • 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-bindi ...

    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.,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.,Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 4 group A member 1
J, A, D, G
87Homo sapiensMutation(s): 0 
Gene Names: NR4A1 (GFRP1, HMR, NAK1)
Find proteins for P22736 (Homo sapiens)
Go to Gene View: NR4A1
Go to UniProtKB:  P22736
Entity ID: 1
MoleculeChainsLengthOrganism
DNAI,F26Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)L,C26Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D, G, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.209 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.822α = 109.98
b = 63.210β = 90.21
c = 91.762γ = 89.54
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references, Derived calculations