2lbd: Difference between revisions

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<StructureSection load='2lbd' size='340' side='right'caption='[[2lbd]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
<StructureSection load='2lbd' size='340' side='right'caption='[[2lbd]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2lbd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LBD FirstGlance]. <br>
<table><tr><td colspan='2'>[[2lbd]] 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=2LBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LBD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=REA:RETINOIC+ACID'>REA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.06&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HUMAN RAR GAMMA A CDNA (NUCLEOTIDES 946 - 1683) ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=REA:RETINOIC+ACID'>REA</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=2lbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lbd OCA], [https://pdbe.org/2lbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lbd RCSB], [https://www.ebi.ac.uk/pdbsum/2lbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lbd ProSAT]</span></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=2lbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lbd OCA], [https://pdbe.org/2lbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lbd RCSB], [https://www.ebi.ac.uk/pdbsum/2lbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lbd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RARG_HUMAN RARG_HUMAN] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, acts mainly as an activator of gene expression due to weak binding to corepressors. Required for limb bud development. In concert with RARA or RARB, required for skeletal growth, matrix homeostasis and growth plate function (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2lbd ConSurf].
</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=2lbd ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The 2.0-A crystal structure of the ligand-binding domain (LBD) of the human retinoic acid receptor (RAR)-gamma bound to all-trans retinoic acid reveals the ligand-binding interactions and suggests an electrostatic guidance mechanism. The overall fold is similar to that of the human RXR-alpha apo-LBD, except for the carboxy-terminal part which folds back towards the LBD core, contributing to the hydrophobic ligand pocket and 'sealing' its entry site. We propose a 'mouse trap' mechanism whereby a ligand-induced conformational transition repositions the amphipathic alpha-helix of the AF-2 activating domain and forms a transcriptionally active receptor.
Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid.,Renaud JP, Rochel N, Ruff M, Vivat V, Chambon P, Gronemeyer H, Moras D Nature. 1995 Dec 14;378(6558):681-9. PMID:7501014<ref>PMID:7501014</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2lbd" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Retinoic acid receptor|Retinoic acid receptor]]
*[[Retinoic acid receptor|Retinoic acid receptor]]
*[[Retinoic acid receptor 3D structures|Retinoic acid receptor 3D structures]]
*[[Retinoic acid receptor 3D structures|Retinoic acid receptor 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Moras, D]]
[[Category: Moras D]]
[[Category: Renaud, J P]]
[[Category: Renaud J-P]]
[[Category: Rochel, N]]
[[Category: Rochel N]]
[[Category: Ruff, M]]
[[Category: Ruff M]]
[[Category: SPINE, Structural Proteomics in Europe]]
[[Category: Active conformation]]
[[Category: All-trans retinoic acid]]
[[Category: Complex]]
[[Category: Holo form]]
[[Category: Ligand-binding domain]]
[[Category: Ligand-dependent]]
[[Category: Nuclear receptor]]
[[Category: Retinoic acid receptor]]
[[Category: Spine]]
[[Category: Structural genomic]]
[[Category: Structural proteomics in europe]]
[[Category: Transcription regulation]]

Latest revision as of 12:04, 21 February 2024

LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO ALL-TRANS RETINOIC ACIDLIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO ALL-TRANS RETINOIC ACID

Structural highlights

2lbd is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.06Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RARG_HUMAN Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, acts mainly as an activator of gene expression due to weak binding to corepressors. Required for limb bud development. In concert with RARA or RARB, required for skeletal growth, matrix homeostasis and growth plate function (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2lbd, resolution 2.06Å

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