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PDBsum entry 1r0o

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protein dna_rna metals Protein-protein interface(s) links
Transcription/DNA PDB id
1r0o
Jmol
Contents
Protein chains
76 a.a. *
78 a.a. *
DNA/RNA
Metals
_ZN ×4
Waters ×279
* Residue conservation analysis
PDB id:
1r0o
Name: Transcription/DNA
Title: Crystal structure of the heterodimeric ecdysone receptor DNA-binding complex
Structure: Ecdysone response element. Chain: c. Engineered: yes. Ecdysone response element. Chain: d. Engineered: yes. Ultraspiracle protein. Chain: a. Fragment: ultraspiracle DNA binding domain.
Source: Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: usp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ecr.
Biol. unit: Tetramer (from PQS)
Resolution:
2.24Å     R-factor:   0.232     R-free:   0.270
Authors: S.Devarakonda,J.M.Harp,Y.Kim,A.Ozyhar,F.Rastinejad
Key ref: S.Devarakonda et al. (2003). Structure of the heterodimeric ecdysone receptor DNA-binding complex. EMBO J, 22, 5827-5840. PubMed id: 14592980
Date:
22-Sep-03     Release date:   21-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20153  (USP_DROME) -  Protein ultraspiracle
Seq:
Struc:
508 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
P34021  (ECR_DROME) -  Ecdysone receptor
Seq:
Struc:
 
Seq:
Struc:
878 a.a.
78 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     6 terms  

 

 
EMBO J 22:5827-5840 (2003)
PubMed id: 14592980  
 
 
Structure of the heterodimeric ecdysone receptor DNA-binding complex.
S.Devarakonda, J.M.Harp, Y.Kim, A.Ozyhar, F.Rastinejad.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18845237 I.Pascual, I.M.Larrayoz, and I.R.Rodriguez (2009).
Retinoic acid regulates the human methionine sulfoxide reductase A (MSRA) gene via two distinct promoters.
  Genomics, 93, 62-71.  
19796154 Y.Nakagawa, and V.C.Henrich (2009).
Arthropod nuclear receptors and their role in molting.
  FEBS J, 276, 6128-6157.  
18271015 C.Nieva, M.Spindler-Barth, and K.D.Spindler (2008).
Impact of heterodimerization on intracellular localization of the ecdysteroid receptor (EcR).
  Arch Insect Biochem Physiol, 68, 40-48.  
18829458 P.Lu, G.B.Rha, M.Melikishvili, G.Wu, B.C.Adkins, M.G.Fried, and Y.I.Chi (2008).
Structural Basis of Natural Promoter Recognition by a Unique Nuclear Receptor, HNF4{alpha}: DIABETES GENE PRODUCT.
  J Biol Chem, 283, 33685-33697.
PDB code: 3cbb
18594514 S.G.Sprecher, and C.Desplan (2008).
Switch of rhodopsin expression in terminally differentiated Drosophila sensory neurons.
  Nature, 454, 533-537.  
18049881 T.Krusiński, M.Wietrzych, I.Grad, A.Ozyhar, and P.Dobryszycki (2008).
Equilibrium Analysis of the DNA Binding Domain of the Ultraspiracle Protein Interaction with the Response Element from the hsp27 Gene Promoter-the Application of Molecular Beacon Technology.
  J Fluoresc, 18, 1.  
17426125 M.Jakób, R.Kołodziejczyk, M.Orłowski, S.Krzywda, A.Kowalska, J.Dutko-Gwóźdź, T.Gwóźdź, M.Kochman, M.Jaskólski, and A.Ozyhar (2007).
Novel DNA-binding element within the C-terminal extension of the nuclear receptor DNA-binding domain.
  Nucleic Acids Res, 35, 2705-2718.
PDB code: 2han
17681172 S.W.Van Mil, A.Milona, P.H.Dixon, R.Mullenbach, V.L.Geenes, J.Chambers, V.Shevchuk, G.E.Moore, F.Lammert, A.G.Glantz, L.A.Mattsson, J.Whittaker, M.G.Parker, R.White, and C.Williamson (2007).
Functional variants of the central bile acid sensor FXR identified in intrahepatic cholestasis of pregnancy.
  Gastroenterology, 133, 507-516.  
16756554 F.Bonneton, F.G.Brunet, J.Kathirithamby, and V.Laudet (2006).
The rapid divergence of the ecdysone receptor is a synapomorphy for Mecopterida that clarifies the Strepsiptera problem.
  Insect Mol Biol, 15, 351-362.  
16525830 J.Börner, T.Puschmann, and C.Duch (2006).
A steroid hormone affects sodium channel expression in Manduca central neurons.
  Cell Tissue Res, 325, 175-187.  
17201771 J.Beatty, T.Fauth, J.L.Callender, M.Spindler-Barth, and V.C.Henrich (2006).
Analysis of transcriptional activity mediated by Drosophila melanogaster ecdysone receptor isoforms in a heterologous cell culture system.
  Insect Mol Biol, 15, 785-795.  
15822096 B.Greb-Markiewicz, T.Fauth, and M.Spindler-Barth (2005).
Ligand binding is without effect on complex formation of the ligand binding domain of the ecdysone receptor (EcR).
  Arch Insect Biochem Physiol, 59, 1.  
15803508 C.Consoulas, R.B.Levine, and L.L.Restifo (2005).
The steroid hormone-regulated gene Broad Complex is required for dendritic growth of motoneurons during metamorphosis of Drosophila.
  J Comp Neurol, 485, 321-337.  
16011476 D.M.Ruden, M.De Luca, M.D.Garfinkel, K.L.Bynum, and X.Lu (2005).
Drosophila nutrigenomics can provide clues to human gene-nutrient interactions.
  Annu Rev Nutr, 25, 499-522.  
16085755 J.E.Donald, and E.I.Shakhnovich (2005).
Predicting specificity-determining residues in two large eukaryotic transcription factor families.
  Nucleic Acids Res, 33, 4455-4465.  
16175536 S.C.Perera, S.Zheng, Q.L.Feng, P.J.Krell, A.Retnakaran, and S.R.Palli (2005).
Heterodimerization of ecdysone receptor and ultraspiracle on symmetric and asymmetric response elements.
  Arch Insect Biochem Physiol, 60, 55-70.  
15037741 P.L.Shaffer, A.Jivan, D.E.Dollins, F.Claessens, and D.T.Gewirth (2004).
Structural basis of androgen receptor binding to selective androgen response elements.
  Proc Natl Acad Sci U S A, 101, 4758-4763.
PDB code: 1r4i
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.