3ww9 - Revision history

OCA at 08:47, 20 March 2024

OCA — Wed, 20 Mar 2024 08:47:32 GMT

←Older revision		Revision as of 08:47, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ww9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ww9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.33Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3ww7\|3ww7]]~~, ~~[[3ww8\|3ww8]], [[3wwa\|3wwa]], [[3wwb\|3wwb]], [[3wwf\|3wwf]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [https://pdbe.org/3ww9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww9 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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [https://pdbe.org/3ww9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww9 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The modular structure of many protein families, such as beta-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical beta-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry.
-
-	Computational design of a self-assembling symmetrical beta-propeller protein.,Voet AR, Noguchi H, Addy C, Simoncini D, Terada D, Unzai S, Park SY, Zhang KY, Tame JR Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15102-7. doi:, 10.1073/pnas.1412768111. Epub 2014 Oct 6. PMID:25288768<ref>PMID:25288768</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3ww9" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Addy, C]]	+	[[Category: Addy C]]
-	[[Category: Noguchi, H]]	+	[[Category: Noguchi H]]
-	[[Category: Park~~, S Y~~]]	+	[[Category: Park SY]]
-	[[Category: Simoncini, D]]	+	[[Category: Simoncini D]]
-	[[Category: Tame~~, J R.H~~]]	+	[[Category: Tame JRH]]
-	[[Category: Terada, D]]	+	[[Category: Terada D]]
-	[[Category: Unzai, S]]	+	[[Category: Unzai S]]
-	[[Category: Voet~~, A R.D~~]]	+	[[Category: Voet ARD]]
-	[[Category: Zhang~~, K Y.J]]~~	+	[[Category: Zhang KYJ]]
-	~~[[Category: Computational protein design]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Self-assembly~~]]	+

OCA at 05:33, 10 August 2022

OCA — Wed, 10 Aug 2022 05:33:42 GMT

←Older revision		Revision as of 05:33, 10 August 2022
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	==Crystal structure of the computationally designed Pizza6 protein==		==Crystal structure of the computationally designed Pizza6 protein==
-	<StructureSection load='3ww9' size='340' side='right' caption='[[3ww9]], [[Resolution\|resolution]] 1.33Å' scene=''>	+	<StructureSection load='3ww9' size='340' side='right'caption='[[3ww9]], [[Resolution\|resolution]] 1.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ww9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WW9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ww9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww7\|3ww7]], [[3ww8\|3ww8]], [[3wwa\|3wwa]], [[3wwb\|3wwb]], [[3wwf\|3wwf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ww7\|3ww7]], [[3ww8\|3ww8]], [[3wwa\|3wwa]], [[3wwb\|3wwb]], [[3wwf\|3wwf]]</div></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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [~~http~~://pdbe.org/3ww9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ww9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww9 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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [https://pdbe.org/3ww9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Addy, C]]		[[Category: Addy, C]]
	[[Category: Noguchi, H]]		[[Category: Noguchi, H]]

OCA at 10:14, 11 August 2016

OCA — Thu, 11 Aug 2016 10:14:35 GMT

←Older revision		Revision as of 10:14, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the computationally designed Pizza6 protein==		==Crystal structure of the computationally designed Pizza6 protein==
	<StructureSection load='3ww9' size='340' side='right' caption='[[3ww9]], [[Resolution\|resolution]] 1.33Å' scene=''>		<StructureSection load='3ww9' size='340' side='right' caption='[[3ww9]], [[Resolution\|resolution]] 1.33Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww7\|3ww7]], [[3ww8\|3ww8]], [[3wwa\|3wwa]], [[3wwb\|3wwb]], [[3wwf\|3wwf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww7\|3ww7]], [[3ww8\|3ww8]], [[3wwa\|3wwa]], [[3wwb\|3wwb]], [[3wwf\|3wwf]]</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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww9 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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [http://pdbe.org/3ww9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3ww9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:05, 25 January 2015

OCA — Sun, 25 Jan 2015 11:05:33 GMT

←Older revision		Revision as of 11:05, 25 January 2015
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Addy, C.]]	+	[[Category: Addy, C]]
-	[[Category: Noguchi, H.]]	+	[[Category: Noguchi, H]]
-	[[Category: Park, S Y.]]	+	[[Category: Park, S Y]]
-	[[Category: Simoncini, D.]]	+	[[Category: Simoncini, D]]
-	[[Category: Tame, J R.H.]]	+	[[Category: Tame, J R.H]]
-	[[Category: Terada, D.]]	+	[[Category: Terada, D]]
-	[[Category: Unzai, S.]]	+	[[Category: Unzai, S]]
-	[[Category: Voet, A R.D.]]	+	[[Category: Voet, A R.D]]
-	[[Category: Zhang, K Y.J.]]	+	[[Category: Zhang, K Y.J]]
	[[Category: Computational protein design]]		[[Category: Computational protein design]]
	[[Category: De novo protein]]		[[Category: De novo protein]]
	[[Category: Self-assembly]]		[[Category: Self-assembly]]

OCA at 07:07, 5 November 2014

OCA — Wed, 05 Nov 2014 07:07:25 GMT

←Older revision		Revision as of 07:07, 5 November 2014
Line 7:		Line 7:
	<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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww9 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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww9 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The modular structure of many protein families, such as beta-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical beta-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry.
		+
		+	Computational design of a self-assembling symmetrical beta-propeller protein.,Voet AR, Noguchi H, Addy C, Simoncini D, Terada D, Unzai S, Park SY, Zhang KY, Tame JR Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15102-7. doi:, 10.1073/pnas.1412768111. Epub 2014 Oct 6. PMID:25288768<ref>PMID:25288768</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:46, 8 October 2014

OCA — Wed, 08 Oct 2014 07:46:29 GMT

←Older revision		Revision as of 07:46, 8 October 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of the computationally designed Pizza6 protein==
-		+	<StructureSection load='3ww9' size='340' side='right' caption='[[3ww9]], [[Resolution\|resolution]] 1.33Å' scene=''>
-	~~The entry~~ 3ww9 is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3ww9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WW9 FirstGlance]. <br>
-	~~Authors~~: ~~Voet~~, A.R.D., ~~Noguchi~~, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., ~~Park, S~~.Y., Zhang, K.Y.J.~~, Tame, J.R.H.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww7\|3ww7]], [[3ww8\|3ww8]], [[3wwa\|3wwa]], [[3wwb\|3wwb]], [[3wwf\|3wwf]]</td></tr>
-	~~Description~~: ~~Crystal structure of the computationally designed Pizza6~~ protein	+	<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=3ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ww9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww9 PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Addy, C.]]
		+	[[Category: Noguchi, H.]]
		+	[[Category: Park, S Y.]]
		+	[[Category: Simoncini, D.]]
		+	[[Category: Tame, J R.H.]]
		+	[[Category: Terada, D.]]
		+	[[Category: Unzai, S.]]
		+	[[Category: Voet, A R.D.]]
		+	[[Category: Zhang, K Y.J.]]
		+	[[Category: Computational protein design]]
		+	[[Category: De novo protein]]
		+	[[Category: Self-assembly]]

OCA: Protected "3ww9" [edit=sysop:move=sysop]

OCA — Wed, 25 Jun 2014 05:33:06 GMT

Protected "3ww9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:33, 25 June 2014

OCA: New page: '''Unreleased structure''' The entry 3ww9 is ON HOLD Authors: Voet, A.R.D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S.Y., Zhang, K.Y.J., Tame, J.R.H. Descrip...

OCA — Wed, 25 Jun 2014 05:33:05 GMT

New page: '''Unreleased structure''' The entry 3ww9 is ON HOLD Authors: Voet, A.R.D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S.Y., Zhang, K.Y.J., Tame, J.R.H. Descrip...

New page

'''Unreleased structure'''

The entry 3ww9 is ON HOLD

Authors: Voet, A.R.D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S.Y., Zhang, K.Y.J., Tame, J.R.H.

Description: Crystal structure of the computationally designed Pizza6 protein