5Y41 | pdb_00005y41

Crystal Structure of LIGAND-BOUND NURR1-LBD

• PDB DOI: https://doi.org/10.2210/pdb5Y41/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-31 Released: 2018-12-26 
• Deposition Author(s): Sreekanth, R., Lescar, J., Yoon, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.253 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.206 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

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 

• PubMed: 32451509 
• DOI: https://doi.org/10.1038/s41589-020-0553-6
• Primary Citation Related Structures: 
  5Y41


• 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-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.

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Organizational Affiliation: 
• School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA.
Department of Biomedical Engineering, Hanyang University, Seoul, Korea.
Paean Biotechnology, Daejeon, Korea.
Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore.
NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
Experimental Drug Development Centre, Agency for Science, Technology and Research, Nanos, Singapore, Singapore.
Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
National Neuroscience Institute, Singapore, Singapore.
Lee Kong Chian School of Medicine, Singapore, Singapore.
Department of Bioscience and Biotechnology, Konkuk University, Gwangjin-gu, Seoul, Republic of Korea.
Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. [e-mail].
NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore. [e-mail].
Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA. [e-mail].
Program in Neuroscience and Harvard Stem Cell Institute, McLean Hospital, Harvard Medical School, Belmont, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.18 kDa 
• Atom Count: 4,082 
• Modeled Residue Count: 464 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 4 group A member 2	A, B	271	Homo sapiens	Mutation(s): 0  Gene Names: NR4A2, NOT, NURR1, TINUR
UniProt & NIH Common Fund Data Resources
Find proteins for P43354 (Homo sapiens) Explore P43354  Go to UniProtKB:  P43354
PHAROS:  P43354 GTEx:  ENSG00000153234

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RPG	C [auth A], H [auth B]	(13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid C20 H32 O4 BGKHCLZFGPIKKU-LDDQNKHRSA-N
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.253 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.206 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.52	α = 90
b = 131.46	β = 90
c = 47.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Sreekanth, R., Lescar, J., Yoon, H.S.

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary