5edn: Difference between revisions
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==Structure of HOXB13-DNA(TCG) complex== | ==Structure of HOXB13-DNA(TCG) complex== | ||
<StructureSection load='5edn' size='340' side='right' caption='[[5edn]], [[Resolution|resolution]] 3.20Å' scene=''> | <StructureSection load='5edn' size='340' side='right'caption='[[5edn]], [[Resolution|resolution]] 3.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5edn]] is a 12 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5edn]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EDN FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5edn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edn OCA], [https://pdbe.org/5edn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5edn RCSB], [https://www.ebi.ac.uk/pdbsum/5edn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5edn ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/HXB13_HUMAN HXB13_HUMAN] Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Jolma A]] | ||
[[Category: | [[Category: Morgunova E]] | ||
[[Category: | [[Category: Popov A]] | ||
[[Category: | [[Category: Taipale J]] | ||
[[Category: | [[Category: Yin Y]] | ||
Latest revision as of 09:22, 5 July 2023
Structure of HOXB13-DNA(TCG) complexStructure of HOXB13-DNA(TCG) complex
Structural highlights
FunctionHXB13_HUMAN Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Publication Abstract from PubMedMost transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (DeltaG). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar DeltaG. However, the interaction with the CAA sequence was driven by change in enthalpy (DeltaH), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (DeltaS). This thermodynamic mechanism that leads to at least two local optima likely affects many macromolecular interactions, as DeltaG depends on two partially independent variables DeltaH and DeltaS according to the central equation of thermodynamics, DeltaG = DeltaH - TDeltaS. Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.,Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J Elife. 2018 Apr 11;7. pii: 32963. doi: 10.7554/eLife.32963. PMID:29638214[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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