7BJU

Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to the synthetic agonist BYI08346


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Nonsteroidal ecdysone receptor agonists use a water channel for binding to the ecdysone receptor complex EcR/USP.

Browning, C.McEwen, A.G.Mori, K.Yokoi, T.Moras, D.Nakagawa, Y.Billas, I.M.L.

(2021) J Pestic Sci 46: 88-100

  • DOI: 10.1584/jpestics.D20-095
  • Primary Citation of Related Structures:  
    7BJU, 7BJV

  • PubMed Abstract: 
  • The ecdysone receptor (EcR) possesses the remarkable capacity to adapt structurally to different types of ligands. EcR binds ecdysteroids, including 20-hydroxyecdysone (20E), as well as nonsteroidal synthetic agonists such as insecticidal dibenzoylhydrazines (DBHs) ...

    The ecdysone receptor (EcR) possesses the remarkable capacity to adapt structurally to different types of ligands. EcR binds ecdysteroids, including 20-hydroxyecdysone (20E), as well as nonsteroidal synthetic agonists such as insecticidal dibenzoylhydrazines (DBHs). Here, we report the crystal structures of the ligand-binding domains of Heliothis virescens EcR/USP bound to the DBH agonist BYI09181 and to the imidazole-type compound BYI08346. The region delineated by helices H7 and H10 opens up to tightly fit a phenyl ring of the ligands to an extent that depends on the bulkiness of ring substituent. In the structure of 20E-bound EcR, this part of the ligand-binding pocket (LBP) contains a channel filled by water molecules that form an intricate hydrogen bond network between 20E and LBP. The water channel present in the nuclear receptor bound to its natural hormone acts as a critical molecular adaptation spring used to accommodate synthetic agonists inside its binding cavity.


    Organizational Affiliation

    Université de Strasbourg, Strasbourg, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ultraspiracle Protein A263Heliothis virescensMutation(s): 0 
Gene Names: B5V51_5554
Find proteins for A0A2A4K9Z3 (Heliothis virescens)
Explore A0A2A4K9Z3 
Go to UniProtKB:  A0A2A4K9Z3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ecdysone Receptor D266Heliothis virescensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPH
Query on EPH

Download Ideal Coordinates CCD File 
A
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
 Ligand Interaction
834
Query on 834

Download Ideal Coordinates CCD File 
D
N-[2-(2-chlorophenyl)-4-methyl-5-(1-methylethyl)-1H-imidazol-1-yl]-5-methyl-2,3-dihydro-1,4-benzodioxine-6-carboxamide
C23 H24 Cl N3 O3
XLNQTHXOKGRTAL-UHFFFAOYSA-N
 Ligand Interaction
PE8
Query on PE8

Download Ideal Coordinates CCD File 
D
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.875α = 90
b = 147.875β = 90
c = 59.776γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release