5w8y - Revision history

OCA at 10:29, 14 June 2023

OCA — Wed, 14 Jun 2023 10:29:09 GMT

←Older revision		Revision as of 10:29, 14 June 2023
Line 1:		Line 1:

	==Solution Structure of XPH1, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds==		==Solution Structure of XPH1, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds==
-	<StructureSection load='5w8y' size='340' side='right'caption='[[5w8y~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5w8y' size='340' side='right'caption='[[5w8y]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w8y]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Xylella_fastidiosa_ann~~-1 Xylella fastidiosa ~~ann~~-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w8y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xylella_fastidiosa_subsp._sandyi_Ann-1 Xylella fastidiosa subsp. sandyi Ann-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W8Y FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D934_07735, D934_08955 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155920 Xylella fastidiosa Ann-1])</td></tr>	+	</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=5w8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8y OCA], [https://pdbe.org/5w8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w8y RCSB], [https://www.ebi.ac.uk/pdbsum/5w8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8y 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=5w8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8y OCA], [~~http~~://pdbe.org/5w8y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w8y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w8y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8y ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A060H7L8_XYLFS A0A060H7L8_XYLFS]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Xylella fastidiosa ~~ann~~-1]]	+	[[Category: Xylella fastidiosa subsp. sandyi Ann-1]]
-	[[Category: Cordes~~, M H~~]]	+	[[Category: Cordes MH]]
-	[[Category: Dykstra~~, E M~~]]	+	[[Category: Dykstra EM]]
-	[[Category: Kumirov~~, V K]]~~	+	[[Category: Kumirov VK]]
-	~~[[Category: Conformational switch]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Helix-turn-helix]]~~	+
-	~~[[Category: Metamorphic protein]]~~	+
-	~~[[Category: Structural evolution]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 09:47, 1 January 2020

OCA — Wed, 01 Jan 2020 09:47:42 GMT

←Older revision		Revision as of 09:47, 1 January 2020
Line 1:		Line 1:

	==Solution Structure of XPH1, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds==		==Solution Structure of XPH1, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds==
-	<StructureSection load='5w8y' size='340' side='right' caption='[[5w8y]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5w8y' size='340' side='right'caption='[[5w8y]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xylella_fastidiosa_ann-1 Xylella fastidiosa ann-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xylella_fastidiosa_ann-1 Xylella fastidiosa ann-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8Y FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Xylella fastidiosa ann-1]]		[[Category: Xylella fastidiosa ann-1]]
	[[Category: Cordes, M H]]		[[Category: Cordes, M H]]

OCA at 22:03, 9 August 2018

OCA — Thu, 09 Aug 2018 22:03:40 GMT

←Older revision		Revision as of 22:03, 9 August 2018
Line 3:		Line 3:
	<StructureSection load='5w8y' size='340' side='right' caption='[[5w8y]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='5w8y' size='340' side='right' caption='[[5w8y]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w8y]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xylella_fastidiosa_ann-1 Xylella fastidiosa ann-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8Y FirstGlance]. <br>
-	</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=5w8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8y OCA], [http://pdbe.org/5w8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w8y RCSB], [http://www.ebi.ac.uk/pdbsum/5w8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8y ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D934_07735, D934_08955 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155920 Xylella fastidiosa Ann-1])</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=5w8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8y OCA], [http://pdbe.org/5w8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w8y RCSB], [http://www.ebi.ac.uk/pdbsum/5w8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8y ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	New protein folds may evolve from existing folds through metamorphic evolution involving a dramatic switch in structure. To mimic pathways by which amino-acid sequence changes could induce a change in fold, we designed two folded hybrids of Xfaso 1 and Pfl 6, a pair of homologous Cro protein sequences with ~40% identity but different folds (all-alpha vs. alpha+beta, respectively). Each hybrid, XPH1 or XPH2, is 85% identical in sequence to its parent, Xfaso 1 or Pfl 6, respectively; 55% identical to its noncognate parent; and ~70% identical to the other hybrid. XPH1 and XPH2 also feature a designed hybrid chameleon sequence corresponding to the C-terminal region, which switched from alpha-helical to beta-sheet structure during Cro evolution. We report solution NMR structures of XPH1 and XPH2 at 0.3 A and 0.5 A backbone RMSD, respectively. XPH1 retains a global fold generally similar to Xfaso 1, and XPH2 retains a fold similar to Pfl 6, as measured by TM-align scores (~0.7), DALI Z-scores (7-9), and backbone RMSD (2-3 A RMSD for the most ordered regions). However, these scores also indicate significant deviations in structure. Most notably, XPH1 and XPH2 have different, and intermediate, secondary structure content relative to Xfaso 1 and Pfl 6. The multistep progression in sequence, from Xfaso 1 to XPH1 to XPH2 to Pfl 6, thus involves both abrupt and gradual changes in folding pattern. The plasticity of some protein folds may allow for "polymetamorphic" evolution through intermediate structures. This article is protected by copyright. All rights reserved.
		+
		+	Multistep mutational transformation of a protein fold through structural intermediates.,Kumirov VK, Dykstra EM, Hall BM, Anderson WJ, Szyszka TN, Cordes MHJ Protein Sci. 2018 Jul 27. doi: 10.1002/pro.3488. PMID:30051937<ref>PMID:30051937</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5w8y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Xylella fastidiosa ann-1]]
	[[Category: Cordes, M H]]		[[Category: Cordes, M H]]
	[[Category: Dykstra, E M]]		[[Category: Dykstra, E M]]

OCA at 05:35, 11 July 2018

OCA — Wed, 11 Jul 2018 05:35:09 GMT

←Older revision		Revision as of 05:35, 11 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5w8y is ON HOLD until Paper Publication~~	+	==Solution Structure of XPH1, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds==
-		+	<StructureSection load='5w8y' size='340' side='right' caption='[[5w8y]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors: Kumirov, V.K., Dykstra, E.M., Cordes, M.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5w8y]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8Y FirstGlance]. <br>
-	~~Description:~~ Solution Structure of XPH1, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds	+	</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=5w8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8y OCA], [http://pdbe.org/5w8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w8y RCSB], [http://www.ebi.ac.uk/pdbsum/5w8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8y ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Kumirov~~, V.K]]	+	__TOC__
-	[[Category: Cordes, M.H]]	+	</StructureSection>
-	[[Category: Dykstra, E.M]]	+	[[Category: Cordes, M H]]
		+	[[Category: Dykstra, E M]]
		+	[[Category: Kumirov, V K]]
		+	[[Category: Conformational switch]]
		+	[[Category: Disulfide bond]]
		+	[[Category: Helix-turn-helix]]
		+	[[Category: Metamorphic protein]]
		+	[[Category: Structural evolution]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]

OCA: Protected "5w8y" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:34:51 GMT

Protected "5w8y" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:34, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w8y is ON HOLD until Paper Publication Authors: Kumirov, V.K., Dykstra, E.M., Cordes, M.H. Description: Solution Structure of XPH1, a Hybrid Seque...

OCA — Wed, 27 Sep 2017 14:34:50 GMT

New page: '''Unreleased structure''' The entry 5w8y is ON HOLD until Paper Publication Authors: Kumirov, V.K., Dykstra, E.M., Cordes, M.H. Description: Solution Structure of XPH1, a Hybrid Seque...

New page

'''Unreleased structure'''

The entry 5w8y is ON HOLD until Paper Publication

Authors: Kumirov, V.K., Dykstra, E.M., Cordes, M.H.

Description: Solution Structure of XPH1, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds
[[Category: Unreleased Structures]]
[[Category: Kumirov, V.K]]
[[Category: Cordes, M.H]]
[[Category: Dykstra, E.M]]