6L6Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 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. --: --

  • DOI: 10.1074/jbc.RA119.010730
  • Primary Citation of Related Structures:  

  • 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 respon ...

    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 (NurREs), namely, an inverted repeat and an everted repeat at 2.6-2.8 Å resolutions.  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

    Central South University, China.,University of Southern California.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor related 1
A, B
85Homo sapiensMutation(s): 0 
Gene Names: NR4A2
Find proteins for F1D8N6 (Homo sapiens)
Go to Gene View: NR4A2
Go to UniProtKB:  F1D8N6
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*TP*GP*AP*CP*CP*TP*TP*TP*AP*AP*AP*GP*GP*TP*CP*AP*CP*T)-3')C,F20Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 35.696α = 90.00
b = 35.696β = 90.00
c = 259.273γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-10-29 
  • Released Date: 2019-11-20 
  • 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: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Database references