4ldx: Difference between revisions

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-{{STRUCTURE_4ldx|  PDB=4ldx  |  SCENE=  }}
+==Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (ARF1) in complex with protomor-like sequence ER7==
-===Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (ARF1) in complex with protomor-like sequence ER7===
+<StructureSection load='4ldx' size='340' side='right' caption='[[4ldx]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-{{ABSTRACT_PUBMED_24485461}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ldx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LDX FirstGlance]. <br>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ldu|4ldu]], [[4ldv|4ldv]], [[4ldw|4ldw]], [[4ldy|4ldy]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARF1, At1g59750, F23H11.7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4ldx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ldx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ldx RCSB], [http://www.ebi.ac.uk/pdbsum/4ldx PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.
-==Function==
+Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors.,Boer DR, Freire-Rios A, van den Berg WA, Saaki T, Manfield IW, Kepinski S, Lopez-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D, Coll M Cell. 2014 Jan 30;156(3):577-89. doi: 10.1016/j.cell.2013.12.027. PMID:24485461<ref>PMID:24485461</ref>
-[[http://www.uniprot.org/uniprot/ARFA_ARATH ARFA_ARATH]] Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Seems to act as transcriptional repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Acts as repressor of IAA2, IAA3 and IAA7.<ref>PMID:12036261</ref> <ref>PMID:16176952</ref>
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[4ldx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LDX OCA].
+</div>
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:024485461</ref><references group="xtra"/><references/>
+__TOC__
-[[Category: Berg, W M.A van den.]]
+</StructureSection>
-[[Category: Boer, D R.]]
+[[Category: Arath]]
-[[Category: Coll, M.]]
+[[Category: Berg, W M.A van den]]
-[[Category: Freire-Rios, A.]]
+[[Category: Boer, D R]]
-[[Category: Weijers, D.]]
+[[Category: Coll, M]]
+[[Category: Freire-Rios, A]]
+[[Category: Weijers, D]]
 [[Category: Nucleus]]
 [[Category: Promotor dna]]