2R40

Crystal structure of 20E bound EcR/USP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Critical Role of Desolvation in the Binding of 20-Hydroxyecdysone to the Ecdysone Receptor

Browning, C.Martin, E.Loch, C.Wurtz, J.M.Moras, D.Stote, R.H.Dejaegere, A.P.Billas, I.M.L.

(2007) J.Biol.Chem. 282: 32924-32934

  • DOI: 10.1074/jbc.M705559200

  • PubMed Abstract: 
  • The insect steroid hormone 20-hydroxyecdysone (20E) binds to its cognate nuclear receptor composed of the ecdysone receptor (EcR) and Ultraspiracle (USP) and triggers the main developmental transitions, in particular molting and metamorphosis. We pre ...

    The insect steroid hormone 20-hydroxyecdysone (20E) binds to its cognate nuclear receptor composed of the ecdysone receptor (EcR) and Ultraspiracle (USP) and triggers the main developmental transitions, in particular molting and metamorphosis. We present the crystal structure of the ligand-binding domains of EcR/USP in complex with 20E at 2.4A resolution and compare it with published structures of EcR/USP bound to ponasterone A (ponA). ponA is essentially identical to 20E but lacks the 25-OH group of 20E. The structure of 20E-bound EcR indicates that an additional hydrogen bond is formed compared with the ponA-bound receptor, yet, paradoxically, ponA has a significantly higher affinity for EcR than 20E. Theoretical studies based on docking and free energy methods lead to a rationale for understanding the difference in binding affinities between 20E and ponA. Results of the calculations indicate that the favorable contribution from the extra H-bond made by 25-OH of 20E is counterbalanced by its larger desolvation cost compared with that of ponA. The contribution of 25-OH to the binding affinity is further compared with those of 20- and 22-OH groups. Ligands that lack the 20- or 22-OH group are indeed known to bind less favorably to EcR than 20E, an effect opposite to that observed for ponA. The results indicate that their respective contributions to receptor-ligand complex stability reside mostly in their different contributions to solvation/desolvation. Together, the data demonstrate the critical role of ligand desolvation in determining binding affinity, with general implications for the binding of hormones to their cognate nuclear receptors.


    Organizational Affiliation

    Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, 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
A
263Heliothis virescensMutation(s): 0 
Find proteins for Q7SIF6 (Heliothis virescens)
Go to UniProtKB:  Q7SIF6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
20E
Query on 20E

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Download CCD File 
D
(2beta,3beta,5beta,22R)-2,3,14,20,22,25-hexahydroxycholest-7-en-6-one
2-beta,3-beta,14,20,22,25-Hexahydroxy-5-beta-cholet-7-en-6- one
C27 H44 O7
NKDFYOWSKOHCCO-YPVLXUMRSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EPH
Query on EPH

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

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Download CCD File 
D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 58.001α = 90.00
b = 58.001β = 90.00
c = 303.592γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
AMoREphasing
ADSCdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description