3u2b: Difference between revisions

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<StructureSection load='3u2b' size='340' side='right'caption='[[3u2b]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='3u2b' size='340' side='right'caption='[[3u2b]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3u2b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U2B FirstGlance]. <br>
<table><tr><td colspan='2'>[[3u2b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U2B FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3f27|3f27]], [[1gt0|1gt0]]</div></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]] 2.402&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Sox4, Sox-4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3u2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u2b OCA], [https://pdbe.org/3u2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u2b RCSB], [https://www.ebi.ac.uk/pdbsum/3u2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u2b 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=3u2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u2b OCA], [https://pdbe.org/3u2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u2b RCSB], [https://www.ebi.ac.uk/pdbsum/3u2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u2b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SOX4_MOUSE SOX4_MOUSE]] Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif.  
[https://www.uniprot.org/uniprot/SOX4_MOUSE SOX4_MOUSE] Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
It has recently been proposed that the sequence preferences of DNA-binding transcription factors can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. Here we present the crystal structure of the high-mobility group (HMG) domain of Sox4 bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2 we observed subtle conformational differences at the DNA binding interface. Furthermore, using quantitative electrophoretic mobility shift assays (EMSAs) we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These data suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adoptions lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.
 
Crystal structure of the Sox4 HMG/DNA complex suggests a mechanism for the positional interdependence in DNA recognition.,Jauch R, Ng CK, Narasimhan K, Kolatkar PR Biochem J. 2011 Dec 19. PMID:22181698<ref>PMID:22181698</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3u2b" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lk3 transgenic mice]]
[[Category: Mus musculus]]
[[Category: Jauch, R]]
[[Category: Jauch R]]
[[Category: Kolatkar, P R]]
[[Category: Kolatkar PR]]
[[Category: Ng, C K.L]]
[[Category: Ng CKL]]
[[Category: Hmg domain]]
[[Category: Transcription-dna complex]]
[[Category: Transcriptional regulation]]

Latest revision as of 11:38, 20 March 2024

Structure of the Sox4 HMG domain bound to DNAStructure of the Sox4 HMG domain bound to DNA

Structural highlights

3u2b is a 3 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.402Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SOX4_MOUSE Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif.

3u2b, resolution 2.40Å

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