6HN6

A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor RXR-ALPHA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor retinoic X receptor alpha.

Eberhardt, J.McEwen, A.G.Bourguet, W.Moras, D.Dejaegere, A.

(2019) Acta Crystallogr F Struct Biol Commun 75: 98-104

  • DOI: 10.1107/S2053230X18018022

  • PubMed Abstract: 
  • The retinoic X receptor (RXR) plays a crucial role in the superfamily of nuclear receptors (NRs) by acting as an obligatory partner of several nuclear receptors; its role as a transcription factor is thus critical in many signalling pathways, such as ...

    The retinoic X receptor (RXR) plays a crucial role in the superfamily of nuclear receptors (NRs) by acting as an obligatory partner of several nuclear receptors; its role as a transcription factor is thus critical in many signalling pathways, such as metabolism, cell development, differentiation and cellular death. The first published structure of the apo ligand-binding domain (LBD) of RXRα, which is still used as a reference today, contained inaccuracies. In the present work, these inaccuracies were corrected using modern crystallographic tools. The most important correction concerns the presence of a π-bulge in helix H7, which was originally built as a regular α-helix. The presence of several CHAPS molecules, which are visible for the first time in the electron-density map and which stabilize the H1-H3 loop, which contains helix H2, are also revealed. The apo RXR structure has played an essential role in deciphering the molecular mode of action of NR ligands and is still used in numerous biophysical studies. This refined structure should be used preferentially in the future in interpreting experiments as well as for modelling and structural dynamics studies of the apo RXRα LBD.


    Related Citations: 
    • Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-alpha.
      Bourguet, W.,Ruff, M.,Chambon, P.,Gronemeyer, H.,Moras, D.
      (1995) Nature 375: 377


    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre de Biochimie Structurale (CBS), CNRS, Inserm, Université de Montpellier, Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A
282Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

Download SDF File 
Download CCD File 
A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
CHAPS
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.173 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 110.800α = 90.00
b = 110.800β = 90.00
c = 109.900γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MLPHAREphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-BINF-003
French National Research AgencyFranceANR-10-IDEX-0002-02
French National Research AgencyFranceANR-10-INBS-05
French National Research AgencyFranceANR-10-LABX-0030-INRT
French National Research AgencyFranceANR-IAB-2011-BIP:BIP

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release