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| | ==Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence== | | ==Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence== |
| - | <StructureSection load='5zjq' size='340' side='right' caption='[[5zjq]], [[Resolution|resolution]] 2.44Å' scene=''> | + | <StructureSection load='5zjq' size='340' side='right'caption='[[5zjq]], [[Resolution|resolution]] 2.44Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zjq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZJQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zjq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZJQ FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Abd-B, CG10291 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME]), exd, CG8933 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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]] 2.443Å</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=5zjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjq OCA], [http://pdbe.org/5zjq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zjq RCSB], [http://www.ebi.ac.uk/pdbsum/5zjq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjq 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=5zjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjq OCA], [https://pdbe.org/5zjq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zjq RCSB], [https://www.ebi.ac.uk/pdbsum/5zjq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ABDB_DROME ABDB_DROME]] Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. [[http://www.uniprot.org/uniprot/EXD_DROME EXD_DROME]] Transcription factor which acts with the selector homeodomain proteins altering the regulation of downstream target genes such as wingless (wg), teashirt (tsh) and decapentaplegic (dpp), thus affecting segmental identity. Delimits the eye field and prevent inappropriate eye development. Required for proper localization of chordotonal organs within the peripheral nervous system.<ref>PMID:8104703</ref> <ref>PMID:8100142</ref> <ref>PMID:7914871</ref> <ref>PMID:9346235</ref> <ref>PMID:9463350</ref> <ref>PMID:9450936</ref> | + | [https://www.uniprot.org/uniprot/ABDB_DROME ABDB_DROME] 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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| | </div> | | </div> |
| | <div class="pdbe-citations 5zjq" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5zjq" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Hox protein|Hox protein]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Drome]] | + | [[Category: Drosophila melanogaster]] |
| - | [[Category: Baburajendran, N]] | + | [[Category: Large Structures]] |
| - | [[Category: Honig, B]] | + | [[Category: Baburajendran N]] |
| - | [[Category: Kaczynska, A]] | + | [[Category: Honig B]] |
| - | [[Category: Mann, R]] | + | [[Category: Kaczynska A]] |
| - | [[Category: Palmer, A G]] | + | [[Category: Mann R]] |
| - | [[Category: Shapiro, L]] | + | [[Category: Palmer AG]] |
| - | [[Category: Zeiske, T]] | + | [[Category: Shapiro L]] |
| - | [[Category: Abdb]]
| + | [[Category: Zeiske T]] |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Exd]]
| + | |
| - | [[Category: Shape]]
| + | |
| - | [[Category: Specificity]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription-dna complex]]
| + | |
| Structural highlights
Function
ABDB_DROME 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 PubMed
Transcription factors bind to their binding sites over a wide range of affinities, yet how differences in affinity are encoded in DNA sequences is not well understood. Here, we report X-ray crystal structures of four heterodimers of the Hox protein AbdominalB bound with its cofactor Extradenticle to four target DNA molecules that differ in affinity by up to approximately 20-fold. Remarkably, despite large differences in affinity, the overall structures are very similar in all four complexes. In contrast, the predicted shapes of the DNA binding sites (i.e., the intrinsic DNA shape) in the absence of bound protein are strikingly different from each other and correlate with affinity: binding sites that must change conformations upon protein binding have lower affinities than binding sites that have more optimal conformations prior to binding. Together, these observations suggest that intrinsic differences in DNA shape provide a robust mechanism for modulating affinity without affecting other protein-DNA interactions.
Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.,Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG 3rd, Shapiro L, Honig B, Mann RS Cell Rep. 2018 Aug 28;24(9):2221-2230. doi: 10.1016/j.celrep.2018.07.100. PMID:30157419[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG 3rd, Shapiro L, Honig B, Mann RS. Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites. Cell Rep. 2018 Aug 28;24(9):2221-2230. doi: 10.1016/j.celrep.2018.07.100. PMID:30157419 doi:http://dx.doi.org/10.1016/j.celrep.2018.07.100
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