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4i1k

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==Crystal Structure of VRN1 (Residues 208-341)==
==Crystal Structure of VRN1 (Residues 208-341)==
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<StructureSection load='4i1k' size='340' side='right' caption='[[4i1k]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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<StructureSection load='4i1k' size='340' side='right'caption='[[4i1k]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4i1k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I1K FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4i1k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I1K FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wid|1wid]], [[1yel|1yel]], [[3hqf|3hqf]]</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=CL:CHLORIDE+ION'>CL</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VRN1, At3g18990, K13E13.10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4i1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1k OCA], [https://pdbe.org/4i1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i1k RCSB], [https://www.ebi.ac.uk/pdbsum/4i1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1k ProSAT]</span></td></tr>
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<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=4i1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i1k RCSB], [http://www.ebi.ac.uk/pdbsum/4i1k PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/VRN1_ARATH VRN1_ARATH]] Involved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner.<ref>PMID:12114624</ref>
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[https://www.uniprot.org/uniprot/VRN1_ARATH VRN1_ARATH] Involved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner.<ref>PMID:12114624</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The B3 DNA binding domain is a plant-specific domain, found throughout the plant kingdom from the alga Chlamydomonas to grasses and flowering plants. Over 100 B3 domain-containing proteins are found in the model plant Arabidopsis thaliana and one of these is critical for accelerating flowering in response to prolonged cold treatment; an epigenetic process called vernalization. Despite the specific phenotype of genetic vrn1 mutants, the VERNALIZATION1 (VRN1) protein localizes throughout the nucleus and in vitro shows sequence non-specific binding. In this work we used a dominant repressor tag that overcomes genetic redundancy to show that VRN1 is involved in processes beyond vernalization that are essential for Arabidopsis development. To understand its sequence non-specific binding we crystallized VRN1208-341 and solved its crystal structure to 1.6 A resolution using Se-SAD methods. The crystallized construct comprises the second VRN1 B3 domain and a preceding region conserved among VRN1 orthologs, but absent in other B3 domains. We established the DNA binding face using NMR then mutated positively charged residues on this surface with a series of 16 Ala and Glu substitutions ensuring the protein fold was not disturbed using HSQC NMR spectra. A triple mutant R249E R289E R296E was almost completely incapable of DNA binding in vitro. Thus, we have revealed that although VRN1 is sequence non-specific in DNA binding, it has a defined DNA binding surface.
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The Arabidopsis B3 domain protein VERNALIZATION1 is involved in processes essential for development with structural and mutational studies revealing its DNA binding surface.,King G, Chanson AH, McCallum EJ, Ohme-Takagi M, Byriel K, Hill JM, Martin JL, Mylne JS J Biol Chem. 2012 Dec 19. PMID:23255593<ref>PMID:23255593</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
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[[Category: Byriel, K]]
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[[Category: Large Structures]]
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[[Category: Chanson, A H]]
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[[Category: Byriel K]]
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[[Category: Hill, J M]]
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[[Category: Chanson AH]]
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[[Category: King, G]]
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[[Category: Hill JM]]
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[[Category: Martin, J L]]
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[[Category: King G]]
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[[Category: McCallum, E J]]
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[[Category: Martin JL]]
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[[Category: Mylne, J S]]
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[[Category: McCallum EJ]]
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[[Category: Ohme-Takagi, M]]
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[[Category: Mylne JS]]
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[[Category: B3 domain beta-barrel]]
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[[Category: Ohme-Takagi M]]
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[[Category: Dna binding protein]]
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Current revision

Crystal Structure of VRN1 (Residues 208-341)

PDB ID 4i1k

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