4RZE | pdb_00004rze

Crystal Structure Analysis of the NUR77 Ligand Binding Domain, L437W,D594E mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.309 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.250 (Depositor) 
  • R-Value Observed: 
    0.253 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4RZE

This is version 1.3 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/nchembio.1788
  • Primary Citation 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.


  • 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.

Macromolecule Content 

  • Total Structure Weight: 57.68 kDa 
  • Atom Count: 3,839 
  • Modeled Residue Count: 461 
  • Deposited Residue Count: 512 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 4 group A member 1A [auth B],
B [auth A]
256Homo sapiensMutation(s): 2 
Gene Names: GFRP1HMRNAK1NR4A1
UniProt & NIH Common Fund Data Resources
Find proteins for P22736 (Homo sapiens)
Explore P22736 
Go to UniProtKB:  P22736
PHAROS:  P22736
GTEx:  ENSG00000123358 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22736
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.309 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.250 (Depositor) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.266α = 90
b = 76.893β = 90
c = 128.518γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
AUTOMARdata reduction
PHASESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description