5Y41

Crystal Structure of LIGAND-BOUND NURR1-LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

PGE1 and PGA1 bind to Nurr1 and activate its transcriptional function.

Rajan, S.Jang, Y.Kim, C.H.Kim, W.Toh, H.T.Jeon, J.Song, B.Serra, A.Lescar, J.Yoo, J.Y.Beldar, S.Ye, H.Kang, C.Liu, X.W.Feitosa, M.Kim, Y.Hwang, D.Goh, G.Lim, K.L.Park, H.M.Lee, C.H.Oh, S.F.Petsko, G.A.Yoon, H.S.Kim, K.S.

(2020) Nat Chem Biol 

  • DOI: 10.1038/s41589-020-0553-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The orphan nuclear receptor Nurr1 is critical for the development, maintenance and protection of midbrain dopaminergic (mDA) neurons. Here we show that prostaglandin E1 (PGE1) and its dehydrated metabolite, PGA1, directly interact with the ligand-bin ...

    The orphan nuclear receptor Nurr1 is critical for the development, maintenance and protection of midbrain dopaminergic (mDA) neurons. Here we show that prostaglandin E1 (PGE1) and its dehydrated metabolite, PGA1, directly interact with the ligand-binding domain (LBD) of Nurr1 and stimulate its transcriptional function. We also report the crystallographic structure of Nurr1-LBD bound to PGA1 at 2.05 Å resolution. PGA1 couples covalently to Nurr1-LBD by forming a Michael adduct with Cys566, and induces notable conformational changes, including a 21° shift of the activation function-2 helix (H12) away from the protein core. Furthermore, PGE1/PGA1 exhibit neuroprotective effects in a Nurr1-dependent manner, prominently enhance expression of Nurr1 target genes in mDA neurons and improve motor deficits in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned mouse models of Parkinson's disease. Based on these results, we propose that PGE1/PGA1 represent native ligands of Nurr1 and can exert neuroprotective effects on mDA neurons, via activation of Nurr1's transcriptional function.


    Organizational Affiliation

    Program in Neuroscience and Harvard Stem Cell Institute, McLean Hospital, Harvard Medical School, Belmont, MA, USA. kskim@mclean.harvard.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 4 group A member 2A, B271Homo 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
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RPG
Query on RPG

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A, B
(13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid
C20 H32 O4
BGKHCLZFGPIKKU-LDDQNKHRSA-N
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.52α = 90
b = 131.46β = 90
c = 47.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references