1R1K

Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to ponasterone A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor.

Billas, I.M.L.Iwema, T.Garnier, J.M.Mitschler, A.Rochel, N.Moras, D.

(2003) Nature 426: 91-96

  • DOI: 10.1038/nature02112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ecdysteroid hormones coordinate the major stages of insect development, notably moulting and metamorphosis, by binding to the ecdysone receptor (EcR); a ligand-inducible nuclear transcription factor. To bind either ligand or DNA, EcR must form a ...

    The ecdysteroid hormones coordinate the major stages of insect development, notably moulting and metamorphosis, by binding to the ecdysone receptor (EcR); a ligand-inducible nuclear transcription factor. To bind either ligand or DNA, EcR must form a heterodimer with ultraspiracle (USP), the homologue of retinoid-X receptor. Here we report the crystal structures of the ligand-binding domains of the moth Heliothis virescens EcR-USP heterodimer in complex with the ecdysteroid ponasterone A and with a non-steroidal, lepidopteran-specific agonist BYI06830 used in agrochemical pest control. The two structures of EcR-USP emphasize the universality of heterodimerization as a general mechanism common to both vertebrates and invertebrates. Comparison of the EcR structures in complex with steroidal and non-steroidal ligands reveals radically different and only partially overlapping ligand-binding pockets that could not be predicted by molecular modelling and docking studies. These findings offer new perspectives for the design of insect-specific, environmentally safe insecticides. The concept of a ligand-dependent binding pocket in EcR provides an insight into the moulding of nuclear receptors to their ligand, and has potential applications for human nuclear receptors.


    Organizational Affiliation

    Département de Biologie et de Génomique Structurales, IGBMC, CNRS/INSERM/Université Louis Pasteur, Parc d'Innovation BP10142, 67404 Illkirch cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ecdysone receptor
D
266Heliothis virescensMutation(s): 0 
Gene Names: EcR (NR1H1)
Find proteins for O18473 (Heliothis virescens)
Go to UniProtKB:  O18473
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ULTRASPIRACLE PROTEIN
A
263Heliothis virescensMutation(s): 0 
Find proteins for Q7SIF6 (Heliothis virescens)
Go to UniProtKB:  Q7SIF6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPH
Query on EPH

Download SDF File 
Download CCD File 
A
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
 Ligand Interaction
P1A
Query on P1A

Download SDF File 
Download CCD File 
D
2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
PONASTERONE A, 25-DEOXYECDYSTERONE, 25-DEOXY-20-HYDROXYECDYSONE,
C27 H44 O6
PJYYBCXMCWDUAZ-JJJZTNILSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.243 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.401α = 90.00
b = 57.401β = 90.00
c = 302.696γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
EPMRphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance