1nq7

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:24, 16 August 2023) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1nq7.gif|left|200px]]
 
-
<!--
+
==Characterization of ligands for the orphan nuclear receptor RORbeta==
-
The line below this paragraph, containing "STRUCTURE_1nq7", creates the "Structure Box" on the page.
+
<StructureSection load='1nq7' size='340' side='right'caption='[[1nq7]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1nq7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NQ7 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARL:7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC+ACID'>ARL</scene></td></tr>
-
{{STRUCTURE_1nq7| PDB=1nq7 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nq7 OCA], [https://pdbe.org/1nq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nq7 RCSB], [https://www.ebi.ac.uk/pdbsum/1nq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nq7 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RORB_RAT RORB_RAT] Orphan nuclear receptor required for normal postnatal development of rod and cone photoreceptor cells. Regulates transcription of OPN1SW in cone photoreceptor cells by binding the sequence 5'-AGGTCA-3' in the OPN1SW promoter.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nq/1nq7_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nq7 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Retinoids regulate gene expression through binding to the nuclear retinoic acid receptors (RARs) and retinoid X receptors (RXRs). In contrast, no ligands for the retinoic acid receptor-related orphan receptors beta and gamma (ROR beta and gamma) have been identified, yet structural data and structure-function analyses indicate that ROR beta is a ligand-regulated nuclear receptor. Using nondenaturing mass spectrometry and scintillation proximity assays we found that all-trans retinoic acid (ATRA) and several retinoids bind to the ROR beta ligand-binding domain (LBD). The crystal structures of the complex with ATRA and with the synthetic analog ALRT 1550 reveal the binding modes of these ligands. ATRA and related retinoids inhibit ROR beta but not ROR alpha transcriptional activity suggesting that high-affinity, subtype-specific ligands could be designed for the identification of ROR beta target genes. Our results identify ROR beta as a retinoid-regulated nuclear receptor, providing a novel pathway for retinoid action.
-
'''Characterization of ligands for the orphan nuclear receptor RORbeta'''
+
All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta.,Stehlin-Gaon C, Willmann D, Zeyer D, Sanglier S, Van Dorsselaer A, Renaud JP, Moras D, Schule R Nat Struct Biol. 2003 Oct;10(10):820-5. Epub 2003 Sep 7. PMID:12958591<ref>PMID:12958591</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
==Overview==
+
</div>
-
A new method was developed for the analysis of pesticide residues in tobacco. The objective was to significantly increase the number of samples that can be processed by the laboratory and to enable the extension of the current coverage to additional pesticides. A new analytical approach was therefore defined based on two main axes, the automation of the sample preparation and the selectivity of the analyte detection using tandem mass spectrometry. This latter aspect reduces the stringency of the requirements placed on the clean-up of the extracts and on the chromatographic resolution when less selective detectors are used. The extraction of the analytes from the matrix is performed using the pressurized liquid extraction technique. Tobacco samples are extracted at elevated temperature and pressure (100 C and 100 atm; 1 atm = 101,325 Pa) using acetone as an extraction solvent. The resulting extract is then concentrated using a Vortex evaporator. Three different solid-phase extraction (SPE) procedures, adjusted to the chemical properties of the different active ingredients to be measured, are applied to the concentrated extract, thus leading to three extract fractions. The first fraction contains such main classes of active ingredients as organohalogenated and 2,6-dinitroaniline compounds while the second one collects the organophosphorus and acylalanines residues; these two fractions are analyzed by capillary gas chromatography coupled to tandem mass spectrometry using negative chemical ionization and electron impact ionization in the positive mode, respectively. The third extract fraction gathers the N-methylcarbamates residues which are analyzed by HPLC with post-column derivatization and fluorescence detection. The different sample preparation stages from extraction to SPE clean-up have been automated through the use of recent analytical technologies. In combination with the analysis by tandem mass spectrometry, this provided a potential for a high sample throughput.
+
<div class="pdbe-citations 1nq7" style="background-color:#fffaf0;"></div>
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1NQ7 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQ7 OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
[[Category: Homo sapiens]]
-
Analysis of multiple pesticide residues in tobacco using pressurized liquid extraction, automated solid-phase extraction clean-up and gas chromatography-tandem mass spectrometry., Haib J, Hofer I, Renaud JM, J Chromatogr A. 2003 Dec 12;1020(2):173-87. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14661742 14661742]
+
[[Category: Large Structures]]
-
[[Category: Protein complex]]
+
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
-
[[Category: Dorsselaer, A Van.]]
+
[[Category: Moras D]]
-
[[Category: Moras, D.]]
+
[[Category: Renaud J-P]]
-
[[Category: Renaud, J P.]]
+
[[Category: Sanglier S]]
-
[[Category: Sanglier, S.]]
+
[[Category: Schuele R]]
-
[[Category: Schuele, R.]]
+
[[Category: Stehlin-Gaon C]]
-
[[Category: Stehlin-Gaon, C.]]
+
[[Category: Van Dorsselaer A]]
-
[[Category: Willmann, D.]]
+
[[Category: Willmann D]]
-
[[Category: Antagonist]]
+
-
[[Category: Ligand-binding domain]]
+
-
[[Category: Retinoic acid]]
+
-
[[Category: Retinoid]]
+
-
[[Category: Synthetic ligand]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:50:53 2008''
+

Current revision

Characterization of ligands for the orphan nuclear receptor RORbeta

PDB ID 1nq7

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nq7"
Personal tools