Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.88 kDa 
• Atom Count: 3821 
• Residue Count: 468 
• Unique protein chains: 1

4RZG

Crystal Structure Analysis of the DNPA-bounded NUR77 Ligand binding Domain

• DOI: 10.2210/pdb4RZG/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-21 Released: 2015-03-18 
• Deposition Author(s): Li, F., Tian, X., Li, A., Li, L., Liu, Y., Chen, H., Wu, Q., Lin, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.270 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Impeding the interaction between Nur77 and p38 reduces LPS-induced inflammation.

Li, L., Liu, Y., Chen, H.Z., Li, F.W., Wu, J.F., Zhang, H.K., He, J.P., Xing, Y.Z., Chen, Y., Wang, W.J., Tian, X.Y., Li, A.Z., Zhang, Q., Huang, P.Q., Han, J., Lin, T., Wu, Q.

(2015) Nat Chem Biol 11: 339-346

• PubMed: 25822914 
• DOI: 10.1038/nchembio.1788
• Primary Citation of Related Structures:  
  4RZE, 4RZF, 4RZG


• PubMed Abstract: 
  

Sepsis, a hyperinflammatory response that can result in multiple organ dysfunctions, is a leading cause of mortality from infection. Here, we show that orphan nuclear receptor Nur77 (also known as TR3) can enhance resistance to lipopolysaccharide (LPS)-induced sepsis in mice by inhibiting NF-κB activity and suppressing aberrant cytokine production. Nur77 directly associates with p65 to block its binding to the κB element. However, this function of Nur77 is countered by the LPS-activated p38α phosphorylation of Nur77. Dampening the interaction between Nur77 and p38α would favor Nur77 suppression of the hyperinflammatory response. A compound, n-pentyl 2-[3,5-dihydroxy-2-(1-nonanoyl) phenyl]acetate, screened from a Nur77-biased library, blocked the Nur77-p38α interaction by targeting the ligand-binding domain of Nur77 and restored the suppression of the hyperinflammatory response through Nur77 inhibition of NF-κB. This study associates the nuclear receptor with immune homeostasis and implicates a new therapeutic strategy to treat hyperinflammatory responses by targeting a p38α substrate to modulate p38α-regulated functions.

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Organizational Affiliation: 

State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 4 group A member 1	A, B	256	Homo sapiens	Mutation(s): 0  Gene Names: GFRP1, HMR, NAK1, NR4A1
Find proteins for P22736 (Homo sapiens) Explore P22736  Go to UniProtKB:  P22736
NIH Common Fund Data Resources
PHAROS  P22736 GTEx  ENSG00000123358

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZHN	A	pentyl (3,5-dihydroxy-2-nonanoylphenyl)acetate C22 H34 O5 FCKDHZVFIMRCNM-UHFFFAOYSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.270 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.228	α = 90
b = 76.529	β = 90
c = 128.677	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-21 
• Released Date: 2015-03-18 
Deposition Author(s): Li, F., Tian, X., Li, A., Li, L., Liu, Y., Chen, H., Wu, Q., Lin, T.

Revision History 

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2015-05-06
  Changes: Database references