1R1K | pdb_00001r1k

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.304 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1038/nature02112
  • Primary Citation Related Structures: 
    1R1K, 1R20

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 61.5 kDa 
  • Atom Count: 3,887 
  • Modeled Residue Count: 477 
  • Deposited Residue Count: 529 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ecdysone receptorA [auth D]266Heliothis virescensMutation(s): 0 
Gene Names: ECR OR NR1H1
UniProt
Find proteins for O18473 (Heliothis virescens)
Explore O18473 
Go to UniProtKB:  O18473
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18473
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ULTRASPIRACLE PROTEINB [auth A]263Heliothis virescensMutation(s): 0 
UniProt
Find proteins for Q7SIF6 (Heliothis virescens)
Explore Q7SIF6 
Go to UniProtKB:  Q7SIF6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIF6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPH

Query on EPH



Download:Ideal Coordinates CCD File
D [auth A]L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
P1A

Query on P1A



Download:Ideal Coordinates CCD File
C [auth D]2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
C27 H44 O6
PJYYBCXMCWDUAZ-JJJZTNILSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.304 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.401α = 90
b = 57.401β = 90
c = 302.696γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary