1a6y: Difference between revisions

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[[Image:1a6y.gif|left|200px]]


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==REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX==
The line below this paragraph, containing "STRUCTURE_1a6y", creates the "Structure Box" on the page.
<StructureSection load='1a6y' size='340' side='right'caption='[[1a6y]], [[Resolution|resolution]] 2.30&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'>[[1a6y]] is a 4 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=1A6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A6Y 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]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_1a6y| PDB=1a6y  | SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1a6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6y OCA], [https://pdbe.org/1a6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a6y RCSB], [https://www.ebi.ac.uk/pdbsum/1a6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a6y ProSAT]</span></td></tr>
 
</table>
'''REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX'''
== Function ==
 
[https://www.uniprot.org/uniprot/NR1D1_HUMAN NR1D1_HUMAN] Functions as a constitutive transcriptional repressor. In collaboration with SP1, activates GJA1 transcription (By similarity). Possible receptor for triiodothyronine.<ref>PMID:2539258</ref> <ref>PMID:1971514</ref>
 
== Evolutionary Conservation ==
==Overview==
[[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/a6/1a6y_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=1a6y ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The nuclear hormone receptors form the largest known family of transcription factors. The current notion of receptor DNA discrimination, based solely on one major type of hexameric half-site and a highly conserved 66-residue core DNA-binding domain (DBD), does not adequately describe how more than 150 nonsteroid receptors differentiate among response elements. Here, we describe the 2.3 A crystal structure of the DNA-binding region of the orphan receptor RevErb arranged as a tandem homodimer on its optimal response element. The structure reveals the presence of a second major protein-DNA interface adjacent to the classical one involving the half-sites. A sequence comparison of orphan receptors suggests that unique minor-groove interactions involving the receptor hinge regions impart the necessary DNA and dimerization specificity.
The nuclear hormone receptors form the largest known family of transcription factors. The current notion of receptor DNA discrimination, based solely on one major type of hexameric half-site and a highly conserved 66-residue core DNA-binding domain (DBD), does not adequately describe how more than 150 nonsteroid receptors differentiate among response elements. Here, we describe the 2.3 A crystal structure of the DNA-binding region of the orphan receptor RevErb arranged as a tandem homodimer on its optimal response element. The structure reveals the presence of a second major protein-DNA interface adjacent to the classical one involving the half-sites. A sequence comparison of orphan receptors suggests that unique minor-groove interactions involving the receptor hinge regions impart the necessary DNA and dimerization specificity.


==About this Structure==
Structural elements of an orphan nuclear receptor-DNA complex.,Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA, Rastinejad F Mol Cell. 1998 May;1(6):849-61. PMID:9660968<ref>PMID:9660968</ref>
1A6Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6Y OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structural elements of an orphan nuclear receptor-DNA complex., Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA, Rastinejad F, Mol Cell. 1998 May;1(6):849-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9660968 9660968]
</div>
<div class="pdbe-citations 1a6y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Khorasanizadeh, S.]]
[[Category: Khorasanizadeh S]]
[[Category: Rastinejad, F.]]
[[Category: Rastinejad F]]
[[Category: Zhao, Q.]]
[[Category: Zhao Q]]
[[Category: Dna-binding]]
[[Category: Nuclear receptor]]
[[Category: Orphan receptor]]
[[Category: Rev-erb]]
[[Category: Reverb]]
[[Category: Transcription regulation]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 09:54:26 2008''

Latest revision as of 13:48, 2 August 2023

REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEXREVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX

Structural highlights

1a6y is a 4 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 2.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NR1D1_HUMAN Functions as a constitutive transcriptional repressor. In collaboration with SP1, activates GJA1 transcription (By similarity). Possible receptor for triiodothyronine.[1] [2]

Evolutionary Conservation

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

Publication Abstract from PubMed

The nuclear hormone receptors form the largest known family of transcription factors. The current notion of receptor DNA discrimination, based solely on one major type of hexameric half-site and a highly conserved 66-residue core DNA-binding domain (DBD), does not adequately describe how more than 150 nonsteroid receptors differentiate among response elements. Here, we describe the 2.3 A crystal structure of the DNA-binding region of the orphan receptor RevErb arranged as a tandem homodimer on its optimal response element. The structure reveals the presence of a second major protein-DNA interface adjacent to the classical one involving the half-sites. A sequence comparison of orphan receptors suggests that unique minor-groove interactions involving the receptor hinge regions impart the necessary DNA and dimerization specificity.

Structural elements of an orphan nuclear receptor-DNA complex.,Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA, Rastinejad F Mol Cell. 1998 May;1(6):849-61. PMID:9660968[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Miyajima N, Horiuchi R, Shibuya Y, Fukushige S, Matsubara K, Toyoshima K, Yamamoto T. Two erbA homologs encoding proteins with different T3 binding capacities are transcribed from opposite DNA strands of the same genetic locus. Cell. 1989 Apr 7;57(1):31-9. PMID:2539258
  2. ↑ Lazar MA, Jones KE, Chin WW. Isolation of a cDNA encoding human Rev-ErbA alpha: transcription from the noncoding DNA strand of a thyroid hormone receptor gene results in a related protein that does not bind thyroid hormone. DNA Cell Biol. 1990 Mar;9(2):77-83. PMID:1971514
  3. ↑ Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA, Rastinejad F. Structural elements of an orphan nuclear receptor-DNA complex. Mol Cell. 1998 May;1(6):849-61. PMID:9660968

1a6y, resolution 2.30Å

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