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1hlz

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CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT

Structural highlights

1hlz 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 2.8Å
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

Most nuclear receptors recognize the same consensus hexameric sequence, AGGTCA. An important question has been how the various members of this transcription factor family distinguish identity features in these closely related DNA sites. We determined structures from several crystal forms of the RevErb-DNA complex and analyzed the patterns of protein-DNA interactions and DNA distortions. We found a significant and consistent DNA distortion at a TA step directly preceding the first consensus 5'-AGGTCA-3' recognition sequence. Importantly, while this base-pair sequence is associated with RevErb's high-affinity sites, there are no sequence-specific contacts formed with the protein. Our study shows that RevErb relies instead on the intrinsic geometry and flexibility of this TA site to make the required fit between the proteins' independent major groove and minor groove binding interactions, which occur on both sides of the TA step. Our findings extend the description of response element discrimination to include a role for sequence-dependent DNA deformations and suggest how other monomeric members of this superfamily, such as NGFI-B, SF-1, and ROR, could also recognize unique geometric features in their DNA targets.

DNA deformability as a recognition feature in the reverb response element.,Sierk ML, Zhao Q, Rastinejad F Biochemistry. 2001 Oct 30;40(43):12833-43. PMID:11669620^[3]

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

References

↑ 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
↑ 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
↑ Sierk ML, Zhao Q, Rastinejad F. DNA deformability as a recognition feature in the reverb response element. Biochemistry. 2001 Oct 30;40(43):12833-43. PMID:11669620

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1hlz"

Categories: Homo sapiens | Large Structures | Rastinejad F | Sierk ML | Zhao Q

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT==
-<StructureSection load='1hlz' size='340' side='right' caption='[[1hlz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='1hlz' size='340' side='right'caption='[[1hlz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1hlz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HLZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1HLZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1hlz]] 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=1HLZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HLZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1a6y|1a6y]], [[1ga5|1ga5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hlz OCA], [http://pdbe.org/1hlz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1hlz RCSB], [http://www.ebi.ac.uk/pdbsum/1hlz PDBsum]</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=1hlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hlz OCA], [https://pdbe.org/1hlz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hlz RCSB], [https://www.ebi.ac.uk/pdbsum/1hlz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hlz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 ==
 [[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/hl/1hlz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hl/1hlz_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/chain_selection.php?pdb_ID=2ata 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=1hlz ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Rastinejad, F]]
+[[Category: Large Structures]]
-[[Category: Sierk, M L]]
+[[Category: Rastinejad F]]
-[[Category: Zhao, Q]]
+[[Category: Sierk ML]]
-[[Category: Dna-binding]]
+[[Category: Zhao Q]]
-[[Category: Nuclear receptor]]
-[[Category: Orphan receptor]]
-[[Category: Rev-erb]]
-[[Category: Reverb]]
-[[Category: Transcription-dna complex]]

1hlz

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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