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PDBsum entry 1g2n

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Gene regulation PDB id
1g2n
Jmol
Contents
Protein chain
246 a.a. *
Ligands
EPH
Waters ×259
* Residue conservation analysis
PDB id:
1g2n
Name: Gene regulation
Title: Crystal structure of the ligand binding domain of the ultraspiracle protein usp, the ortholog of rxrs in insects
Structure: Ultraspiracle protein. Chain: a. Fragment: ligand binding domain. Engineered: yes
Source: Heliothis virescens. Tobacco budworm. Organism_taxid: 7102. Gene: usp locus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.65Å     R-factor:   0.210     R-free:   0.244
Authors: I.M.L.Billas,L.Moulinier,N.Rochel,D.Moras,Structural Proteomics In Europe (Spine)
Key ref:
I.M.Billas et al. (2001). Crystal structure of the ligand-binding domain of the ultraspiracle protein USP, the ortholog of retinoid X receptors in insects. J Biol Chem, 276, 7465-7474. PubMed id: 11053444 DOI: 10.1074/jbc.M008926200
Date:
20-Oct-00     Release date:   21-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7SIF6  (Q7SIF6_HELVI) -  Gene regulation protein
Seq:
Struc:
264 a.a.
246 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     steroid hormone mediated signaling pathway   3 terms 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1074/jbc.M008926200 J Biol Chem 276:7465-7474 (2001)
PubMed id: 11053444  
 
 
Crystal structure of the ligand-binding domain of the ultraspiracle protein USP, the ortholog of retinoid X receptors in insects.
I.M.Billas, L.Moulinier, N.Rochel, D.Moras.
 
  ABSTRACT  
 
The major postembryonic developmental events happening in insect life, including molting and metamorphosis, are regulated and coordinated temporally by pulses of ecdysone. The biological activity of this steroid hormone is mediated by two nuclear receptors: the ecdysone receptor (EcR) and the Ultraspiracle protein (USP). The crystal structure of the ligand-binding domain from the lepidopteran Heliothis virescens USP reported here shows that the loop connecting helices H1 and H3 precludes the canonical agonist conformation. The key residues that stabilize this unique loop conformation are strictly conserved within the lepidopteran USP family. The presence of an unexpected bound ligand that drives an unusual antagonist conformation confirms the induced-fit mechanism accompanying the ligand binding. The ligand-binding pocket exhibits a retinoid X receptor-like anchoring part near a conserved arginine, which could interact with a USP ligand functional group. The structure of this receptor provides the template for designing inhibitors, which could be utilized as a novel type of environmentally safe insecticides.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. The ligand-binding pocket and the USP ligand. A, detailed view showing the phospholipid ligand and the residues inside the pocket. Residues closer than 4.0 Å from the ligand are depicted in blue and labeled accordingly. Polar residues inside the cavity, which do not interact with the ligand, are shown in green and indicated with green labels. The phospholipid ligand is colored in gray for carbon, red for oxygen, and green for phosphor atom. The protein backbone is colored in dark yellow. H3, H5, H6, H7, H10, and L1-3 are indicated. B, view showing the location of the phospholipid molecule in the ligand-binding pocket of USP relative to that of 9-cis-RA in the RXR cavity. The phospholipid ligand and the 9-cis-RA are colored in gray and blue. The conserved arginine belonging to H5 is also shown in this figure as a ball and stick representation. The color scheme for the atoms is: gray, carbon; red, oxygen; green, phosphor; blue, nitrogen. C, a stereo view of the superimposition of USP/phospholipid and RXRa/9-cis-RA in the region of the conserved arginine belonging to helix H5. The protein backbones of USP and RXR are represented by orange and blue ribbons, respectively. The phospholipid ligand is depicted in yellow, and the 9-cis-RA is colored in light gray for carbon, blue for nitrogen, and red for oxygen. Residues belonging to RXR are shown in blue, while those of USP are colored in light gray for carbon, blue for nitrogen, and red for oxygen. Water molecules are drawn as red spheres, and hydrogen bonds are depicted as green dotted lines. A few key residues are labeled in blue for RXR and in black for USP.
Figure 5.
Fig. 5. View of the superimposition of the ligand-binding pockets of USP/phospholipid and RXR /9-cis-RA. The ligand cavities of USP and RXR are depicted in light blue and magenta, respectively. The occupation of both cavities by their respective ligand is shown by transparency. The probe-occupied ligand-binding cavity is calculated by MSMS with a probe radius of 1.4 Å. The oxygen and phosphorus atoms are colored in red and light gray, respectively, and the carbon atoms are colored in yellow for the phospholipid ligand and in green for the 9-cis-RA. The position of a few structural elements of USP is indicated by labels. This figure was prepared using the program DINO (42).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 7465-7474) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20882396 M.Cellanetti, V.Gunda, L.Wang, A.Macchiarulo, and R.Pellicciari (2010).
Insights into the binding mode and mechanism of action of some atypical retinoids as ligands of the small heterodimer partner (SHP).
  J Comput Aided Mol Des, 24, 943-956.  
19646743 M.V.Chakravarthy, I.J.Lodhi, L.Yin, R.R.Malapaka, H.E.Xu, J.Turk, and C.F.Semenkovich (2009).
Identification of a physiologically relevant endogenous ligand for PPARalpha in liver.
  Cell, 138, 476-488.  
19126866 T.Iwema, A.Chaumot, R.A.Studer, M.Robinson-Rechavi, I.M.Billas, D.Moras, V.Laudet, and F.Bonneton (2009).
Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects.
  Mol Biol Evol, 26, 753-768.  
19796154 Y.Nakagawa, and V.C.Henrich (2009).
Arthropod nuclear receptors and their role in molting.
  FEBS J, 276, 6128-6157.  
18342247 F.Bonneton, A.Chaumot, and V.Laudet (2008).
Annotation of Tribolium nuclear receptors reveals an increase in evolutionary rate of a network controlling the ecdysone cascade.
  Insect Biochem Mol Biol, 38, 416-429.  
18348179 G.Markov, G.Lecointre, B.Demeneix, and V.Laudet (2008).
The "street light syndrome", or how protein taxonomy can bias experimental manipulations.
  Bioessays, 30, 349-357.  
18606996 S.M.Nowickyj, J.V.Chithalen, D.Cameron, M.G.Tyshenko, M.Petkovich, G.R.Wyatt, G.Jones, and V.K.Walker (2008).
Locust retinoid X receptors: 9-Cis-retinoic acid in embryos from a primitive insect.
  Proc Natl Acad Sci U S A, 105, 9540-9545.  
17673910 T.Iwema, I.M.Billas, Y.Beck, F.Bonneton, H.Nierengarten, A.Chaumot, G.Richards, V.Laudet, and D.Moras (2007).
Structural and functional characterization of a novel type of ligand-independent RXR-USP receptor.
  EMBO J, 26, 3770-3782.
PDB code: 2nxx
18028192 Y.Nakagawa, A.Sakai, F.Magata, T.Ogura, M.Miyashita, and H.Miyagawa (2007).
Molecular cloning of the ecdysone receptor and the retinoid X receptor from the scorpion Liocheles australasiae.
  FEBS J, 274, 6191-6203.  
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.  
  16841469 M.Szécsi, and M.Spindler-Barth (2006).
Flash labeling of a nuclear receptor domain (D domain of ultraspiracle) fused to tetracysteine tag.
  Acta Biol Hung, 57, 181-190.  
16087883 A.Tan, H.Tanaka, T.Tamura, and T.Shiotsuki (2005).
Precocious metamorphosis in transgenic silkworms overexpressing juvenile hormone esterase.
  Proc Natl Acad Sci U S A, 102, 11751-11756.  
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.  
15660250 D.C.Hayward, J.W.Trueman, M.J.Bastiani, and E.E.Ball (2005).
The structure of the USP/RXR of Xenos pecki indicates that Strepsiptera are not closely related to Diptera.
  Dev Genes Evol, 215, 213-219.  
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.  
15723037 E.A.Ortlund, Y.Lee, I.H.Solomon, J.M.Hager, R.Safi, Y.Choi, Z.Guan, A.Tripathy, C.R.Raetz, D.P.McDonnell, D.D.Moore, and M.R.Redinbo (2005).
Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP.
  Nat Struct Mol Biol, 12, 357-363.
PDB code: 1yuc
15707893 I.N.Krylova, E.P.Sablin, J.Moore, R.X.Xu, G.M.Waitt, J.A.MacKay, D.Juzumiene, J.M.Bynum, K.Madauss, V.Montana, L.Lebedeva, M.Suzawa, J.D.Williams, S.P.Williams, R.K.Guy, J.W.Thornton, R.J.Fletterick, T.M.Willson, and H.A.Ingraham (2005).
Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1.
  Cell, 120, 343-355.
PDB codes: 1ymt 1yok 1yow
16051145 J.Reinking, M.M.Lam, K.Pardee, H.M.Sampson, S.Liu, P.Yang, S.Williams, W.White, G.Lajoie, A.Edwards, and H.M.Krause (2005).
The Drosophila nuclear receptor e75 contains heme and is gas responsive.
  Cell, 122, 195-207.  
15803199 K.King-Jones, and C.S.Thummel (2005).
Nuclear receptors--a perspective from Drosophila.
  Nat Rev Genet, 6, 311-323.  
15373804 A.R.Barchuk, R.Maleszka, and Z.L.Simões (2004).
Apis mellifera ultraspiracle: cDNA sequence and rapid up-regulation by juvenile hormone.
  Insect Mol Biol, 13, 459-467.  
15246430 G.Benoit, M.Malewicz, and T.Perlmann (2004).
Digging deep into the pockets of orphan nuclear receptors: insights from structural studies.
  Trends Cell Biol, 14, 369-376.  
14977043 S.Przibilla, W.W.Hitchcock, M.Szécsi, M.Grebe, J.Beatty, V.C.Henrich, and M.Spindler-Barth (2004).
Functional studies on the ligand-binding domain of Ultraspiracle from Drosophila melanogaster.
  Biol Chem, 385, 21-30.  
12665583 B.Farboud, H.Hauksdottir, Y.Wu, and M.L.Privalsky (2003).
Isotype-restricted corepressor recruitment: a constitutively closed helix 12 conformation in retinoic acid receptors beta and gamma interferes with corepressor recruitment and prevents transcriptional repression.
  Mol Cell Biol, 23, 2844-2858.  
14519121 C.Minakuchi, Y.Nakagawa, M.Kamimura, and H.Miyagawa (2003).
Binding affinity of nonsteroidal ecdysone agonists against the ecdysone receptor complex determines the strength of their molting hormonal activity.
  Eur J Biochem, 270, 4095-4104.  
12931010 D.Marsh (2003).
Lipid-binding proteins: structure of the phospholipid ligands.
  Protein Sci, 12, 2109-2117.  
12820970 E.P.Sablin, I.N.Krylova, R.J.Fletterick, and H.A.Ingraham (2003).
Structural basis for ligand-independent activation of the orphan nuclear receptor LRH-1.
  Mol Cell, 11, 1575-1585.
PDB code: 1pk5
14498828 F.M.Sladek (2003).
Nuclear receptors as drug targets: new developments in coregulators, orphan receptors and major therapeutic areas.
  Expert Opin Ther Targets, 7, 679-684.  
14595375 I.M.Billas, T.Iwema, J.M.Garnier, A.Mitschler, N.Rochel, and D.Moras (2003).
Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor.
  Nature, 426, 91-96.
PDB codes: 1r1k 1r20
12809604 K.D.Baker, L.M.Shewchuk, T.Kozlova, M.Makishima, A.Hassell, B.Wisely, J.A.Caravella, M.H.Lambert, J.L.Reinking, H.Krause, C.S.Thummel, T.M.Willson, and D.J.Mangelsdorf (2003).
The Drosophila orphan nuclear receptor DHR38 mediates an atypical ecdysteroid signaling pathway.
  Cell, 113, 731-742.
PDB code: 1pdu
12649431 N.Potier, I.M.Billas, A.Steinmetz, C.Schaeffer, A.van Dorsselaer, D.Moras, and J.P.Renaud (2003).
Using nondenaturing mass spectrometry to detect fortuitous ligands in orphan nuclear receptors.
  Protein Sci, 12, 725-733.  
12220494 G.B.Wisely, A.B.Miller, R.G.Davis, A.D.Thornquest, R.Johnson, T.Spitzer, A.Sefler, B.Shearer, J.T.Moore, A.B.Miller, T.M.Willson, and S.P.Williams (2002).
Hepatocyte nuclear factor 4 is a transcription factor that constitutively binds fatty acids.
  Structure, 10, 1225-1234.
PDB code: 1lv2
11864604 H.Greschik, J.M.Wurtz, S.Sanglier, W.Bourguet, A.van Dorsselaer, D.Moras, and J.P.Renaud (2002).
Structural and functional evidence for ligand-independent transcriptional activation by the estrogen-related receptor 3.
  Mol Cell, 9, 303-313.
PDB code: 1kv6
11729082 J.W.Truman, and L.M.Riddiford (2002).
Endocrine insights into the evolution of metamorphosis in insects.
  Annu Rev Entomol, 47, 467-500.  
12079488 L.D.Graham (2002).
Ecdysone-controlled expression of transgenes.
  Expert Opin Biol Ther, 2, 525-535.  
12411578 M.B.Kumar, T.Fujimoto, D.W.Potter, Q.Deng, and S.R.Palli (2002).
A single point mutation in ecdysone receptor leads to increased ligand specificity: implications for gene switch applications.
  Proc Natl Acad Sci U S A, 99, 14710-14715.  
12242296 M.Desclozeaux, I.N.Krylova, F.Horn, R.J.Fletterick, and H.A.Ingraham (2002).
Phosphorylation and intramolecular stabilization of the ligand binding domain in the nuclear receptor steroidogenic factor 1.
  Mol Cell Biol, 22, 7193-7203.  
  15455045 P.C.Bourne, P.Whiting, T.S.Dhadialla, R.E.Hormann, J.P.Girault, J.Harmatha, R.Lafont, and L.Dinan (2002).
Ecdysteroid 7,9(11)-dien-6-ones as potential photoaffinity labels for ecdysteroid binding proteins.
  J Insect Sci, 2, 11.  
  15455059 S.Sasorith, I.M.Billas, T.Iwema, D.Moras, and J.M.Wurtz (2002).
Structure-based analysis of the ultraspiracle protein and docking studies of putative ligands.
  J Insect Sci, 2, 25.  
12473098 Y.Xu, F.Fang, Y.Chu, D.Jones, and G.Jones (2002).
Activation of transcription through the ligand-binding pocket of the orphan nuclear receptor ultraspiracle.
  Eur J Biochem, 269, 6026-6036.  
11689423 C.Stehlin, J.M.Wurtz, A.Steinmetz, E.Greiner, R.Schüle, D.Moras, and J.P.Renaud (2001).
X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation.
  EMBO J, 20, 5822-5831.
PDB code: 1k4w
11607933 U.Egner, N.Heinrich, M.Ruff, M.Gangloff, A.Mueller-Fahrnow, and J.M.Wurtz (2001).
Different ligands-different receptor conformations: modeling of the hER alpha LBD in complex with agonists and antagonists.
  Med Res Rev, 21, 523-539.  
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.