4dzn - Revision history

OCA at 08:45, 21 September 2022

OCA — Wed, 21 Sep 2022 08:45:06 GMT

←Older revision		Revision as of 08:45, 21 September 2022
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	<StructureSection load='4dzn' size='340' side='right'caption='[[4dzn]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='4dzn' size='340' side='right'caption='[[4dzn]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dzn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DZN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dzn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DZN FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dzk\|4dzk]], [[4dzl\|4dzl]], [[4dzm\|4dzm]]~~</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=4dzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dzn OCA], [https://pdbe.org/4dzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dzn RCSB], [https://www.ebi.ac.uk/pdbsum/4dzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dzn 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=4dzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dzn OCA], [~~http~~://pdbe.org/4dzn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dzn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dzn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dzn ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Brady, R L~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Bruning, M~~]]	+	[[Category: Brady RL]]
-	[[Category: ~~Thomson, A R~~]]	+	[[Category: Bruning M]]
-	[[Category: ~~Woolfson, D N~~]]	+	[[Category: Thomson AR]]
-	[[Category: ~~Zaccai, N R~~]]	+	[[Category: Woolfson DN]]
-	[[Category: ~~De novo protein~~]]	+	[[Category: Zaccai NR]]

OCA at 16:46, 28 August 2019

OCA — Wed, 28 Aug 2019 16:46:06 GMT

←Older revision		Revision as of 16:46, 28 August 2019
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	==A de novo designed Coiled Coil CC-pIL==		==A de novo designed Coiled Coil CC-pIL==
-	<StructureSection load='4dzn' size='340' side='right' caption='[[4dzn]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='4dzn' size='340' side='right'caption='[[4dzn]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dzn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DZN FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dzn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DZN FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Brady, R L]]		[[Category: Brady, R L]]
	[[Category: Bruning, M]]		[[Category: Bruning, M]]

OCA at 13:51, 11 August 2016

OCA — Thu, 11 Aug 2016 13:51:20 GMT

←Older revision		Revision as of 13:51, 11 August 2016
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		+
	==A de novo designed Coiled Coil CC-pIL==		==A de novo designed Coiled Coil CC-pIL==
	<StructureSection load='4dzn' size='340' side='right' caption='[[4dzn]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='4dzn' size='340' side='right' caption='[[4dzn]], [[Resolution\|resolution]] 1.59Å' scene=''>
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	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dzk\|4dzk]], [[4dzl\|4dzl]], [[4dzm\|4dzm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dzk\|4dzk]], [[4dzl\|4dzl]], [[4dzm\|4dzm]]</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=4dzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dzn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dzn RCSB], [http://www.ebi.ac.uk/pdbsum/4dzn PDBsum]</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=4dzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dzn OCA], [http://pdbe.org/4dzn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dzn RCSB], [http://www.ebi.ac.uk/pdbsum/4dzn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dzn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4dzn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:06, 25 January 2015

OCA — Sun, 25 Jan 2015 08:06:44 GMT

←Older revision		Revision as of 08:06, 25 January 2015
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-	~~{{STRUCTURE_4dzn\| PDB=4dzn \| SCENE= }}~~	+	==A de novo designed Coiled Coil CC-pIL==
-	===A de novo designed Coiled Coil CC-pIL===	+	<StructureSection load='4dzn' size='340' side='right' caption='[[4dzn]], [[Resolution\|resolution]] 1.59Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23651206}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4dzn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DZN FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dzk\|4dzk]], [[4dzl\|4dzl]], [[4dzm\|4dzm]]</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=4dzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dzn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dzn RCSB], [http://www.ebi.ac.uk/pdbsum/4dzn PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such components should be highly defined and predictable in all respects of sequence, structure, stability, interactions, and function. To establish one such toolkit, here we present a basis set of de novo designed alpha-helical coiled-coil peptides that adopt defined and well-characterized parallel dimeric, trimeric, and tetrameric states. The designs are based on sequence-to-structure relationships both from the literature and analysis of a database of known coiled-coil X-ray crystal structures. These give foreground sequences to specify the targeted oligomer state. A key feature of the design process is that sequence positions outside of these sites are considered non-essential for structural specificity; as such, they are referred to as the background, are kept non-descript, and are available for mutation as required later. Synthetic peptides were characterized in solution by circular-dichroism spectroscopy and analytical ultracentrifugation, and their structures were determined by X-ray crystallography. Intriguingly, a hitherto widely used empirical rule-of-thumb for coiled-coil dimer specification does not hold in the designed system. However, the desired oligomeric state is achieved by database-informed redesign of that particular foreground and confirmed experimentally. We envisage that the basis set will be of use in directing and controlling protein assembly, with potential applications in chemical and synthetic biology. To help with such endeavors, we introduce Pcomp, an on-line registry of peptide components for protein-design and synthetic-biology applications.

-	~~==About this Structure==~~	+	A basis set of de novo coiled-coil Peptide oligomers for rational protein design and synthetic biology.,Fletcher JM, Boyle AL, Bruning M, Bartlett GJ, Vincent TL, Zaccai NR, Armstrong CT, Bromley EH, Booth PJ, Brady RL, Thomson AR, Woolfson DN ACS Synth Biol. 2012 Jun 15;1(6):240-50. doi: 10.1021/sb300028q. Epub 2012 May, 14. PMID:23651206<ref>PMID:23651206</ref>
-	~~[[4dzn]] is a 3 chain structure~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4DZN OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023651206</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Brady, R L.]]	+	== References ==
-	[[Category: Bruning, M.]]	+	<references/>
-	[[Category: Thomson, A R.]]	+	__TOC__
-	[[Category: Woolfson, D N.]]	+	</StructureSection>
-	[[Category: Zaccai, N R.]]	+	[[Category: Brady, R L]]
		+	[[Category: Bruning, M]]
		+	[[Category: Thomson, A R]]
		+	[[Category: Woolfson, D N]]
		+	[[Category: Zaccai, N R]]
	[[Category: De novo protein]]		[[Category: De novo protein]]

OCA at 08:48, 19 June 2013

OCA — Wed, 19 Jun 2013 08:48:30 GMT

←Older revision		Revision as of 08:48, 19 June 2013
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-	[[Image:4dzn.jpg\|left\|200px]]
-
	{{STRUCTURE_4dzn\| PDB=4dzn \| SCENE= }}		{{STRUCTURE_4dzn\| PDB=4dzn \| SCENE= }}
-
	===A de novo designed Coiled Coil CC-pIL===		===A de novo designed Coiled Coil CC-pIL===
-		+	{{ABSTRACT_PUBMED_23651206}}

	==About this Structure==		==About this Structure==
	[[4dzn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA].		[[4dzn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023651206</ref><references group="xtra"/><references/>
	[[Category: Brady, R L.]]		[[Category: Brady, R L.]]
	[[Category: Bruning, M.]]		[[Category: Bruning, M.]]

OCA at 05:22, 29 August 2012

OCA — Wed, 29 Aug 2012 05:22:51 GMT

←Older revision		Revision as of 05:22, 29 August 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:4dzn.jpg\|left\|200px]]

-	~~The entry~~ 4dzn ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4dzn\| PDB=4dzn \| SCENE= }}

-	~~Authors: Bruning, M., Thomson,~~ A~~.R., Zaccai, N.R., Brady, R.L., Woolfson, D.N.~~	+	===A de novo designed Coiled Coil CC-pIL===

-	~~Description~~: A de novo ~~designed Coiled Coil CC-pIL~~	+
		+	==About this Structure==
		+	[[4dzn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZN OCA].
		+	[[Category: Brady, R L.]]
		+	[[Category: Bruning, M.]]
		+	[[Category: Thomson, A R.]]
		+	[[Category: Woolfson, D N.]]
		+	[[Category: Zaccai, N R.]]
		+	[[Category: De novo protein]]

OCA at 07:28, 18 April 2012

OCA — Wed, 18 Apr 2012 07:28:13 GMT

←Older revision		Revision as of 07:28, 18 April 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dzn is ON HOLD	+	The entry 4dzn is ON HOLD until Paper Publication

	Authors: Bruning, M., Thomson, A.R., Zaccai, N.R., Brady, R.L., Woolfson, D.N.		Authors: Bruning, M., Thomson, A.R., Zaccai, N.R., Brady, R.L., Woolfson, D.N.

	Description: A de novo designed Coiled Coil CC-pIL		Description: A de novo designed Coiled Coil CC-pIL

OCA at 06:14, 14 March 2012

OCA — Wed, 14 Mar 2012 06:14:08 GMT

←Older revision		Revision as of 06:14, 14 March 2012
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	The entry 4dzn is ON HOLD		The entry 4dzn is ON HOLD

-	Authors: Bruning M, Thomson AR, Zaccai NR, Brady RL, Woolfson DN	+	Authors: Bruning, M., Thomson, A.R., Zaccai, N.R., Brady, R.L., Woolfson, D.N.

	Description: A de novo designed Coiled Coil CC-pIL		Description: A de novo designed Coiled Coil CC-pIL

OCA: Protected "4dzn" [edit=sysop:move=sysop]

OCA — Thu, 08 Mar 2012 05:31:06 GMT

Protected "4dzn" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:31, 8 March 2012

OCA: New page: '''Unreleased structure''' The entry 4dzn is ON HOLD Authors: Bruning M, Thomson AR, Zaccai NR, Brady RL, Woolfson DN Description: A de novo designed Coiled Coil CC-pIL

OCA — Thu, 08 Mar 2012 05:31:05 GMT

New page: '''Unreleased structure''' The entry 4dzn is ON HOLD Authors: Bruning M, Thomson AR, Zaccai NR, Brady RL, Woolfson DN Description: A de novo designed Coiled Coil CC-pIL

New page

'''Unreleased structure'''

The entry 4dzn is ON HOLD

Authors: Bruning M, Thomson AR, Zaccai NR, Brady RL, Woolfson DN

Description: A de novo designed Coiled Coil CC-pIL