6KZ5

Crystal Structure Analysis of the Csn-B-bounded NUR77 Ligand binding Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.45 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Blocking PPAR gamma interaction facilitates Nur77 interdiction of fatty acid uptake and suppresses breast cancer progression.

Yang, P.B.Hou, P.P.Liu, F.Y.Hong, W.B.Chen, H.Z.Sun, X.Y.Li, P.Zhang, Y.Ju, C.Y.Luo, L.J.Wu, S.F.Zhou, J.X.Wang, Z.J.He, J.P.Li, L.Zhao, T.J.Deng, X.Lin, T.Wu, Q.

(2020) Proc Natl Acad Sci U S A 117: 27412-27422

  • DOI: https://doi.org/10.1073/pnas.2002997117
  • Primary Citation of Related Structures:  
    6KZ5

  • PubMed Abstract: 

    Nuclear receptor Nur77 participates in multiple metabolic regulations and plays paradoxical roles in tumorigeneses. Herein, we demonstrated that the knockout of Nur77 stimulated mammary tumor development in two mouse models, which would be reversed by a specific reexpression of Nur77 in mammary tissues. Mechanistically, Nur77 interacted and recruited corepressors, the SWI/SNF complex, to the promoters of CD36 and FABP4 to suppress their transcriptions, which hampered the fatty acid uptake, leading to the inhibition of cell proliferation. Peroxisome proliferator-activated receptor-γ (PPARγ) played an antagonistic role in this process through binding to Nur77 to facilitate ubiquitin ligase Trim13-mediated ubiquitination and degradation of Nur77. Cocrystallographic and functional analysis revealed that Csn-B, a Nur77-targeting compound, promoted the formation of Nur77 homodimer to prevent PPARγ binding by steric hindrance, thereby strengthening the Nur77's inhibitory role in breast cancer. Therefore, our study reveals a regulatory function of Nur77 in breast cancer via impeding fatty acid uptake.


  • Organizational Affiliation

    State Key Laboratory of Cellular Stress Biology, State-Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, 361005 Xiamen, Fujian Province, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 4 group A member 1
A, B
257Homo sapiensMutation(s): 0 
Gene Names: NR4A1GFRP1HMRNAK1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E4L (Subject of Investigation/LOI)
Query on E4L

Download Ideal Coordinates CCD File 
C [auth B]ethyl 2-[2-octanoyl-3,5-bis(oxidanyl)phenyl]ethanoate
C18 H26 O5
UVVWQQKSNZLUQA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.45 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.589α = 90
b = 76.099β = 90
c = 127.736γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description