5MK4

Crystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol derivative 7 and a fragment of the TIF2 co-activator.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Ligand Dependent Switch from RXR Homo- to RXR-NURR1 Heterodimerization.

Scheepstra, M.Andrei, S.A.de Vries, R.M.J.M.Meijer, F.A.Ma, J.N.Burstein, E.S.Olsson, R.Ottmann, C.Milroy, L.G.Brunsveld, L.

(2017) ACS Chem Neurosci 8: 2065-2077

  • DOI: 10.1021/acschemneuro.7b00216
  • Primary Citation of Related Structures:  
    5MJ5, 5MK4, 5MKJ, 5MKU, 5MMW

  • PubMed Abstract: 
  • Retinoid X receptors (RXRs) play key roles in many physiological processes in both the periphery and central nervous system. In addition, RXRs form heterodimers with other nuclear receptors to exert their physiological effects. The nuclear receptor related 1 protein (NURR1) is particularly interesting because of its role in promoting differentiation and survival of dopamine neurons ...

    Retinoid X receptors (RXRs) play key roles in many physiological processes in both the periphery and central nervous system. In addition, RXRs form heterodimers with other nuclear receptors to exert their physiological effects. The nuclear receptor related 1 protein (NURR1) is particularly interesting because of its role in promoting differentiation and survival of dopamine neurons. However, only a small number of RXR-heterodimer selective modulators are available, with limited chemical diversity. This work describes the synthesis, biochemical evaluation, and structural elucidation of a novel series of RXR ligands with strongly biased interactions with RXRα-NURR1 heterodimers. Targeted modifications to the small molecule biaryl scaffold caused local RXRα side-chain disturbances and displacement of secondary structural elements upon ligand binding. This resulted in the repositioning of protein helices in the heterodimer interface of RXRα, alterations in homo- versus heterodimer formation, and modulation of activation function 2 (AF2). The data provide a rationale for the design of RXR ligands consisting of a highly conserved hydrophilic region, strongly contributing to the ligand affinity, and a variable hydrophobic region, which efficiently probes the effects of structural changes at the level of the ligand on co-regulator recruitment or the RXRα-NURR1 dimerization interface.


    Organizational Affiliation

    Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Technische Universiteit Eindhoven , Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA, C229Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B, D11Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I5W
Query on I5W

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
(~{E})-3-[3-(2-methyl-5-phenyl-phenyl)-4-oxidanyl-phenyl]prop-2-enoic acid
C22 H18 O3
ZVBMBUNLXBSQPU-FMIVXFBMSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
H [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.699α = 90
b = 74.14β = 90
c = 99.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NWONetherlandsECHO 711011017

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references, Derived calculations