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: 10.1016/j.chembiol.2019.02.002
  • Structures With Same Primary Citation

  • 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 ne ...

    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

    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA. Electronic address: pamela.england@ucsf.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 4 group A member 2B, C272Homo sapiensMutation(s): 0 
Gene Names: NR4A2NOTNURR1TINUR
Find proteins for P43354 (Homo sapiens)
Explore P43354 
Go to UniProtKB:  P43354
NIH Common Fund Data Resources
PHAROS  P43354
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 4 group A member 2A272Homo sapiensMutation(s): 0 
Gene Names: NR4A2NOTNURR1TINUR
Find proteins for P43354 (Homo sapiens)
Explore P43354 
Go to UniProtKB:  P43354
NIH Common Fund Data Resources
PHAROS  P43354
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G7J
Query on G7J

Download CCD File 
A, B, C
5-hydroxy-1,2-dihydro-6H-indol-6-one
C8 H7 N O2
RWEUJNADLANQCX-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download CCD File 
A, C
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
AL-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 

  • 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