1R0O | pdb_00001r0o

Crystal Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex

• PDB DOI: https://doi.org/10.2210/pdb1R0O/pdb
• NAKB: 1R0O

• Classification: Transcription/DNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-09-22 Released: 2003-10-21 
• Deposition Author(s): Devarakonda, S., Harp, J.M., Kim, Y., Ozyhar, A., Rastinejad, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.270 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex

Devarakonda, S., Harp, J.M., Kim, Y., Ozyhar, A., Rastinejad, F.

(2003) EMBO J 22: 5827-5840

• PubMed: 14592980 
• DOI: https://doi.org/10.1093/emboj/cdg569
• Primary Citation Related Structures: 
  1R0N, 1R0O


• PubMed Abstract: 
  

  Ecdysteroids initiate molting and metamorphosis in insects via a heterodimeric receptor consisting of the ecdysone receptor (EcR) and ultraspiracle (USP). The EcR-USP heterodimer preferentially mediates transcription through highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp (IR-1). The requirement for a heterodimeric arrangement of EcR-USP subunits to bind to a symmetric DNA is unusual within the nuclear receptor superfamily. We describe the 2.24 A structure of the EcR-USP DNA-binding domain (DBD) heterodimer bound to an idealized IR-1 element. EcR and USP use similar surfaces, and rely on the deformed minor groove of the DNA to establish protein-protein contacts. As retinoid X receptor (RXR) is the mammalian homolog of USP, we also solved the 2.60 A crystal structure of the EcR-RXR DBD heterodimer on IR-1 and found the dimerization and DNA-binding interfaces to be the same as in the EcR-USP complex. Sequence alignments indicate that the EcR-RXR heterodimer is an important model for understanding how the FXR-RXR heterodimer binds to IR-1 sites.

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Organizational Affiliation: 
• Department of Pharmacology, University of Virginia Health System, Charlottesville, VA 22908, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.9 kDa 
• Atom Count: 2,240 
• Modeled Residue Count: 190 
• Deposited Residue Count: 231 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ultraspiracle protein	C [auth A]	86	Drosophila melanogaster	Mutation(s): 0  Gene Names: USP
UniProt
Find proteins for P20153 (Drosophila melanogaster) Explore P20153  Go to UniProtKB:  P20153

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ecdysone receptor	D [auth B]	109	Drosophila melanogaster	Mutation(s): 0  Gene Names: ECR
UniProt
Find proteins for P34021 (Drosophila melanogaster) Explore P34021  Go to UniProtKB:  P34021

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Ecdysone Response Element	A [auth C]	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Ecdysone Response Element	B [auth D]	18	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.270 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.37	α = 90
b = 59.88	β = 90
c = 113.77	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-21 
Deposition Author(s): Devarakonda, S., Harp, J.M., Kim, Y., Ozyhar, A., Rastinejad, F.

Revision History  

• Version 1.0: 2003-10-21
  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