5edn - Revision history

OCA at 06:22, 5 July 2023

OCA — Wed, 05 Jul 2023 06:22:21 GMT

←Older revision		Revision as of 06:22, 5 July 2023
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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 [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. 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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EDN FirstGlance]. <br>	+	<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='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=TRS:2~~-~~AMINO-2-HYDROXYMETHYL-PROPANE-1~~,3~~-DIOL'>TRS</scene>~~</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]] 3.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HOXB13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5edn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edn OCA], [~~http~~://pdbe.org/5edn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5edn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5edn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5edn 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=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 ==
-	[~~[http~~://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.	+	[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 ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Jolma, A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Morgunova, E~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Popov,~~ A]]	+	[[Category: Jolma A]]
-	[[Category: ~~Taipale, J~~]]	+	[[Category: Morgunova E]]
-	[[Category: ~~Yin, Y~~]]	+	[[Category: Popov A]]
-	[[Category: ~~Complex~~]]	+	[[Category: Taipale J]]
-	[[Category: ~~Dna]]~~	+	[[Category: Yin Y]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 16:27, 15 August 2018

OCA — Wed, 15 Aug 2018 16:27:51 GMT

←Older revision		Revision as of 16:27, 15 August 2018
Line 3:		Line 3:
	<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. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EDN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5edn]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EDN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HOXB13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5edn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edn OCA], [http://pdbe.org/5edn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edn RCSB], [http://www.ebi.ac.uk/pdbsum/5edn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5edn ProSAT]</span></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=5edn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edn OCA], [http://pdbe.org/5edn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edn RCSB], [http://www.ebi.ac.uk/pdbsum/5edn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5edn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://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.		[[http://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;">
		+	== Publication Abstract from PubMed ==
		+	Most 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<ref>PMID:29638214</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5edn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hox protein\|Hox protein]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Jolma, A]]		[[Category: Jolma, A]]
	[[Category: Morgunova, E]]		[[Category: Morgunova, E]]

OCA at 19:44, 9 December 2016

OCA — Fri, 09 Dec 2016 19:44:36 GMT

←Older revision		Revision as of 19:44, 9 December 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5edn is ~~ON HOLD until Paper Publication~~	+	==Structure of HOXB13-DNA(TCG) complex==
-		+	<StructureSection load='5edn' size='340' side='right' caption='[[5edn]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~Authors~~: ~~Morgunova, E~~., ~~Yin~~, Y., ~~Jolma, A~~., ~~Popov, A~~., ~~Taipale, J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5edn]] is a 12 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EDN FirstGlance]. <br>
-	~~Description~~: ~~Structure~~ of ~~HOXB13~~-~~DNA(TCG) complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5edn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edn OCA], [http://pdbe.org/5edn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edn RCSB], [http://www.ebi.ac.uk/pdbsum/5edn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5edn ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Jolma, A]]
		+	[[Category: Morgunova, E]]
	[[Category: Popov, A]]		[[Category: Popov, A]]
-	[[Category: ~~Jolma~~, A]]	+	[[Category: Taipale, J]]
	[[Category: Yin, Y]]		[[Category: Yin, Y]]
-	[[Category: ~~Taipale, J~~]]	+	[[Category: Complex]]
-	[[Category: ~~Morgunova, E~~]]	+	[[Category: Dna]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]

OCA at 10:44, 19 October 2016

OCA — Wed, 19 Oct 2016 10:44:00 GMT

←Older revision		Revision as of 10:44, 19 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5edn is ON HOLD	+	The entry 5edn is ON HOLD until Paper Publication

	Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.		Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

OCA at 10:16, 3 October 2016

OCA — Mon, 03 Oct 2016 10:16:13 GMT

←Older revision		Revision as of 10:16, 3 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5edn is ON HOLD ~~until Paper Publication~~	+	The entry 5edn is ON HOLD

	Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.		Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

OCA at 22:15, 10 May 2016

OCA — Tue, 10 May 2016 22:15:21 GMT

←Older revision		Revision as of 22:15, 10 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5edn is ON HOLD	+	The entry 5edn is ON HOLD until Paper Publication

	Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.		Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

OCA: Protected "5edn" [edit=sysop:move=sysop]

OCA — Tue, 01 Dec 2015 02:41:30 GMT

Protected "5edn" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:41, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5edn is ON HOLD Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J. Description: Structure of HOXB13-DNA(TCG) complex [[Category: Un...

OCA — Tue, 01 Dec 2015 02:41:29 GMT

New page: '''Unreleased structure''' The entry 5edn is ON HOLD Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J. Description: Structure of HOXB13-DNA(TCG) complex [[Category: Un...

New page

'''Unreleased structure'''

The entry 5edn is ON HOLD

Authors: Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

Description: Structure of HOXB13-DNA(TCG) complex
[[Category: Unreleased Structures]]
[[Category: Popov, A]]
[[Category: Jolma, A]]
[[Category: Yin, Y]]
[[Category: Taipale, J]]
[[Category: Morgunova, E]]