4zv6 - Revision history

OCA at 11:34, 9 May 2024

OCA — Thu, 09 May 2024 11:34:02 GMT

←Older revision		Revision as of 11:34, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zv6]] is a 2 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=4ZV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZV6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zv6]] is a 2 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=4ZV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZV6 FirstGlance]. <br>
-	</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=4zv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv6 OCA], [https://pdbe.org/4zv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zv6 RCSB], [https://www.ebi.ac.uk/pdbsum/4zv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv6 ProSAT]</span></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]] 2.22Å</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=4zv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv6 OCA], [https://pdbe.org/4zv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zv6 RCSB], [https://www.ebi.ac.uk/pdbsum/4zv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:42, 18 May 2023

OCA — Thu, 18 May 2023 07:42:57 GMT

←Older revision		Revision as of 07:42, 18 May 2023
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	<StructureSection load='4zv6' size='340' side='right'caption='[[4zv6]], [[Resolution\|resolution]] 2.22Å' scene=''>		<StructureSection load='4zv6' size='340' side='right'caption='[[4zv6]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zv6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZV6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZV6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zv6]] is a 2 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=4ZV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZV6 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=4zv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv6 OCA], [~~http~~://pdbe.org/4zv6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zv6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zv6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv6 ProSAT]</span></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=4zv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv6 OCA], [https://pdbe.org/4zv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zv6 RCSB], [https://www.ebi.ac.uk/pdbsum/4zv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv6 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: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Figueroa, M]]	+	[[Category: Figueroa M]]
-	[[Category: Martial~~, J A~~]]	+	[[Category: Martial JA]]
-	[[Category: Minard, P]]	+	[[Category: Minard P]]
-	[[Category: Sleutel, M]]	+	[[Category: Sleutel M]]
-	[[Category: Urvoas, A]]	+	[[Category: Urvoas A]]
-	[[Category: Valerio-Lepiniec, M]]	+	[[Category: Valerio-Lepiniec M]]
-	[[Category: Weerdt, C ~~van de]]~~	+	[[Category: Van de Weerdt C]]
-	~~[[Category: Artificial protein]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Rossmann-like]]~~	+
-	~~[[Category: Synthetic gene~~]]	+

OCA at 08:53, 26 June 2019

OCA — Wed, 26 Jun 2019 08:53:13 GMT

←Older revision		Revision as of 08:53, 26 June 2019
Line 1:		Line 1:

	==Crystal structure of the artificial alpharep-7 octarellinV.1 complex==		==Crystal structure of the artificial alpharep-7 octarellinV.1 complex==
-	<StructureSection load='4zv6' size='340' side='right' caption='[[4zv6]], [[Resolution\|resolution]] 2.22Å' scene=''>	+	<StructureSection load='4zv6' size='340' side='right'caption='[[4zv6]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZV6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zv6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZV6 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=4zv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv6 OCA], [http://pdbe.org/4zv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv6 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv6 PDBsum]</span></td></tr>	+	</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=4zv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv6 OCA], [http://pdbe.org/4zv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv6 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Figueroa, M]]		[[Category: Figueroa, M]]
	[[Category: Martial, J A]]		[[Category: Martial, J A]]

OCA at 22:52, 1 June 2016

OCA — Wed, 01 Jun 2016 22:52:06 GMT

←Older revision		Revision as of 22:52, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4zv6 is ~~ON HOLD~~	+	==Crystal structure of the artificial alpharep-7 octarellinV.1 complex==
		+	<StructureSection load='4zv6' size='340' side='right' caption='[[4zv6]], [[Resolution\|resolution]] 2.22Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4zv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZV6 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=4zv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv6 OCA], [http://pdbe.org/4zv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv6 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv6 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (alphabetaalpha) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features.

-	~~Authors: Figueroa~~, M., Sleutel, M., ~~Urvoas~~, A., Valerio-Lepiniec, M., ~~Minard~~, P., ~~Martial~~, J.A., ~~van~~ de Weerdt, C.	+	The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.,Figueroa M, Sleutel M, Vandevenne M, Parvizi G, Attout S, Jacquin O, Vandenameele J, Fischer AW, Damblon C, Goormaghtigh E, Valerio-Lepiniec M, Urvoas A, Durand D, Pardon E, Steyaert J, Minard P, Maes D, Meiler J, Matagne A, Martial JA, Van de Weerdt C J Struct Biol. 2016 May 12. pii: S1047-8477(16)30089-2. doi:, 10.1016/j.jsb.2016.05.004. PMID:27181418<ref>PMID:27181418</ref>

-	~~Description: Crystal structure~~ of the ~~artificial alpharep-7 octarellinV~~.~~1 complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Sleutel, M]]~~	+	<div class="pdbe-citations 4zv6" style="background-color:#fffaf0;"></div>
-	~~[[Category: Van De Weerdt, C]]~~	+	== References ==
-	~~[[Category: Martial, J.A]]~~	+	<references/>
-	~~[[Category: Urvoas, A]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Figueroa, M]]		[[Category: Figueroa, M]]
		+	[[Category: Martial, J A]]
	[[Category: Minard, P]]		[[Category: Minard, P]]
		+	[[Category: Sleutel, M]]
		+	[[Category: Urvoas, A]]
	[[Category: Valerio-Lepiniec, M]]		[[Category: Valerio-Lepiniec, M]]
		+	[[Category: Weerdt, C van de]]
		+	[[Category: Artificial protein]]
		+	[[Category: De novo protein]]
		+	[[Category: Rossmann-like]]
		+	[[Category: Synthetic gene]]

OCA at 00:12, 1 December 2015

OCA — Tue, 01 Dec 2015 00:12:34 GMT

←Older revision		Revision as of 00:12, 1 December 2015
Line 7:		Line 7:
	Description: Crystal structure of the artificial alpharep-7 octarellinV.1 complex		Description: Crystal structure of the artificial alpharep-7 octarellinV.1 complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Martial, J.A]]
-	[[Category: Urvoas, A]]
-	[[Category: Valerio-Lepiniec, M]]
	[[Category: Sleutel, M]]		[[Category: Sleutel, M]]
	[[Category: Van De Weerdt, C]]		[[Category: Van De Weerdt, C]]
		+	[[Category: Martial, J.A]]
		+	[[Category: Urvoas, A]]
	[[Category: Figueroa, M]]		[[Category: Figueroa, M]]
	[[Category: Minard, P]]		[[Category: Minard, P]]
		+	[[Category: Valerio-Lepiniec, M]]

OCA: Protected "4zv6" [edit=sysop:move=sysop]

OCA — Wed, 27 May 2015 14:45:39 GMT

Protected "4zv6" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:45, 27 May 2015

OCA: New page: '''Unreleased structure''' The entry 4zv6 is ON HOLD Authors: Figueroa, M., Sleutel, M., Urvoas, A., Valerio-Lepiniec, M., Minard, P., Martial, J.A., van de Weerdt, C. Description: Cry...

OCA — Wed, 27 May 2015 14:45:38 GMT

New page: '''Unreleased structure''' The entry 4zv6 is ON HOLD Authors: Figueroa, M., Sleutel, M., Urvoas, A., Valerio-Lepiniec, M., Minard, P., Martial, J.A., van de Weerdt, C. Description: Cry...

New page

'''Unreleased structure'''

The entry 4zv6 is ON HOLD

Authors: Figueroa, M., Sleutel, M., Urvoas, A., Valerio-Lepiniec, M., Minard, P., Martial, J.A., van de Weerdt, C.

Description: Crystal structure of the artificial alpharep-7 octarellinV.1 complex
[[Category: Unreleased Structures]]
[[Category: Martial, J.A]]
[[Category: Urvoas, A]]
[[Category: Valerio-Lepiniec, M]]
[[Category: Sleutel, M]]
[[Category: Van De Weerdt, C]]
[[Category: Figueroa, M]]
[[Category: Minard, P]]