This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.


Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1upw

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:55, 13 December 2023) (edit) (undo)
 
(20 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1upw.gif|left|200px]]<br />
 
-
<applet load="1upw" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1upw, resolution 2.40&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF THE HUMAN LIVER X RECEPTOR BETA LIGAND BINDING DOMAIN IN COMPLEX WITH A SYNTHETIC AGONIST'''<br />
 
-
==Overview==
+
==Crystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist==
-
LXRbeta belongs to the nuclear hormone receptor superfamily of, ligand-activated transcription factors. Its natural ligands are supposed, to be oxidised derivatives of cholesterol. Stimulation of LXRbeta by, agonists activates a number of genes that are involved in the regulation, of lipid metabolism and cholesterol efflux from cells. Therefore, LXRbeta, may represent a novel therapeutic target for the treatment of dyslipidemia, and atherosclerosis.Here, we report the X-ray crystal structure of the, LXRbeta ligand-binding domain in complex with a synthetic agonist, T-0901317. This compound occupies the ligand-binding pocket of the, receptor, forms numerous lipophilic contacts with the protein and one, crucial hydrogen bond to His435 and stabilises the agonist conformation of, the receptor ... [[http://ispc.weizmann.ac.il/pmbin/getpm?14643652 (full description)]]
+
<StructureSection load='1upw' size='340' side='right'caption='[[1upw]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1upw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UPW FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=444:N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE'>444</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1upw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upw OCA], [https://pdbe.org/1upw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1upw RCSB], [https://www.ebi.ac.uk/pdbsum/1upw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1upw ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/NR1H2_HUMAN NR1H2_HUMAN] Orphan receptor. Binds preferentially to double-stranded oligonucleotide direct repeats having the consensus half-site sequence 5'-AGGTCA-3' and 4-nt spacing (DR-4). Regulates cholesterol uptake through MYLIP-dependent ubiquitination of LDLR, VLDLR and LRP8 (By similarity).
 +
== 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/up/1upw_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=1upw ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
LXRbeta belongs to the nuclear hormone receptor superfamily of ligand-activated transcription factors. Its natural ligands are supposed to be oxidised derivatives of cholesterol. Stimulation of LXRbeta by agonists activates a number of genes that are involved in the regulation of lipid metabolism and cholesterol efflux from cells. Therefore, LXRbeta may represent a novel therapeutic target for the treatment of dyslipidemia and atherosclerosis.Here, we report the X-ray crystal structure of the LXRbeta ligand-binding domain in complex with a synthetic agonist, T-0901317. This compound occupies the ligand-binding pocket of the receptor, forms numerous lipophilic contacts with the protein and one crucial hydrogen bond to His435 and stabilises the agonist conformation of the receptor ligand-binding domain. The recruitment of the AF2-region of the protein is not achieved via direct polar interactions of the ligand with protein side-chains of this helical segment, but rather via few hydrophobic contacts and probably more importantly via indirect effects involving the pre-orientation of side-chains that surround the ligand-binding pocket and form the interface to the AF2-helix.On the basis of these results we propose a binding mode and a mechanism of action for the putative natural ligands, oxidised derivatives of cholesterol.
-
==About this Structure==
+
Crystal structure of the human liver X receptor beta ligand-binding domain in complex with a synthetic agonist.,Hoerer S, Schmid A, Heckel A, Budzinski RM, Nar H J Mol Biol. 2003 Dec 12;334(5):853-61. PMID:14643652<ref>PMID:14643652</ref>
-
1UPW is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]] with 444 as [[http://en.wikipedia.org/wiki/ligand ligand]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UPW OCA]].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Crystal structure of the human liver X receptor beta ligand-binding domain in complex with a synthetic agonist., Hoerer S, Schmid A, Heckel A, Budzinski RM, Nar H, J Mol Biol. 2003 Dec 12;334(5):853-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14643652 14643652]
+
</div>
-
[[Category: Homo sapiens]]
+
<div class="pdbe-citations 1upw" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Budzinski, R.M.]]
+
-
[[Category: Heckel, A.]]
+
-
[[Category: Hoerer, S.]]
+
-
[[Category: Nar, H.]]
+
-
[[Category: Schmid, A.]]
+
-
[[Category: 444]]
+
-
[[Category: crystal structure]]
+
-
[[Category: ligand binding domain]]
+
-
[[Category: liver x receptor]]
+
-
[[Category: nuclear hormone receptor]]
+
-
[[Category: transcription factor]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 13:20:39 2007''
+
==See Also==
 +
*[[Liver X receptor|Liver X receptor]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Homo sapiens]]
 +
[[Category: Large Structures]]
 +
[[Category: Budzinski RM]]
 +
[[Category: Heckel A]]
 +
[[Category: Hoerer S]]
 +
[[Category: Nar H]]
 +
[[Category: Schmid A]]

Current revision

Crystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist

PDB ID 1upw

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools