6DDA

Nurr1 Covalently Modified by a Dopamine Metabolite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.

Bruning, J.M.Wang, Y.Oltrabella, F.Tian, B.Kholodar, S.A.Liu, H.Bhattacharya, P.Guo, S.Holton, J.M.Fletterick, R.J.Jacobson, M.P.England, P.M.

(2019) Cell Chem Biol 26: 674-685.e6

  • DOI: https://doi.org/10.1016/j.chembiol.2019.02.002
  • Primary Citation of Related Structures:  
    6DDA

  • PubMed Abstract: 

    Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for Parkinson's disease, a neurological disorder characterized by the degeneration of these same neurons. Efforts to identify Nurr1 agonists have been hampered by the recognition that it lacks several classic regulatory elements of nuclear receptor function, including the canonical ligand-binding pocket. Here we report that the dopamine metabolite 5,6-dihydroxyindole (DHI) binds directly to and modulates the activity of Nurr1. Using biophysical assays and X-ray crystallography, we show that DHI binds to the ligand-binding domain within a non-canonical pocket, forming a covalent adduct with Cys566. In cultured cells and zebrafish, DHI stimulates Nurr1 activity, including the transcription of target genes underlying dopamine homeostasis. These findings suggest avenues for developing synthetic Nurr1 ligands to ameliorate the symptoms and progression of Parkinson's disease.


  • Organizational Affiliation

    Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 4 group A member 2A [auth B],
C
272Homo sapiensMutation(s): 0 
Gene Names: NR4A2NOTNURR1TINUR
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 4 group A member 2B [auth A]272Homo sapiensMutation(s): 0 
Gene Names: NR4A2NOTNURR1TINUR
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G7J
Query on G7J

Download Ideal Coordinates CCD File 
E [auth B],
M [auth A],
R [auth C]
5-hydroxy-1,2-dihydro-6H-indol-6-one
C8 H7 N O2
RWEUJNADLANQCX-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
N [auth C]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth C],
O [auth C],
P [auth C]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
K
Query on K

Download Ideal Coordinates CCD File 
D [auth B],
F [auth B],
K [auth A],
L [auth A],
Q [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
B [auth A]L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.250 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.586α = 90
b = 80.586β = 90
c = 225.805γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Author supporting evidence, Data collection