6wxo - Revision history

OCA at 14:47, 6 March 2024

OCA — Wed, 06 Mar 2024 14:47:25 GMT

←Older revision		Revision as of 14:47, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6wxo' size='340' side='right'caption='[[6wxo]], [[Resolution\|resolution]] 1.41Å' scene=''>		<StructureSection load='6wxo' size='340' side='right'caption='[[6wxo]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6wxo]] 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=6WXO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WXO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wxo]] 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=6WXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WXO 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]] 1.41Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow: auto; max-height~~: ~~3em;~~'>~~[[6wvs\|6wvs]]~~, ~~[[4pww\|4pww]], [[6wxp\|6wxp]]~~</~~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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6wxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wxo OCA], [~~http~~://pdbe.org/6wxo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wxo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wxo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wxo 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=6wxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wxo OCA], [https://pdbe.org/6wxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wxo RCSB], [https://www.ebi.ac.uk/pdbsum/6wxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wxo ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	De novo protein design has succeeded in generating a large variety of globular proteins, but the construction of protein scaffolds with cavities that could accommodate large signaling molecules, cofactors, and substrates remains an outstanding challenge. The long, often flexible loops that form such cavities in many natural proteins are difficult to precisely program and thus challenging for computational protein design. Here we describe an alternative approach to this problem. We fused two stable proteins with C2 symmetry-a de novo designed dimeric ferredoxin fold and a de novo designed TIM barrel-such that their symmetry axes are aligned to create scaffolds with large cavities that can serve as binding pockets or enzymatic reaction chambers. The crystal structures of two such designs confirm the presence of a 420 cubic Angstrom chamber defined by the top of the designed TIM barrel and the bottom of the ferredoxin dimer. We functionalized the scaffold by installing a metal-binding site consisting of four glutamate residues close to the symmetry axis. The protein binds lanthanide ions with very high affinity as demonstrated by tryptophan-enhanced terbium luminescence. This approach can be extended to other metals and cofactors, making this scaffold a modular platform for the design of binding proteins and biocatalysts.
-
-	Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion.,Caldwell SJ, Haydon IC, Piperidou N, Huang PS, Bick MJ, Sjostrom HS, Hilvert D, Baker D, Zeymer C Proc Natl Acad Sci U S A. 2020 Nov 17. pii: 2008535117. doi:, 10.1073/pnas.2008535117. PMID:33203677<ref>PMID:33203677</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6wxo" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Caldwell~~, S J~~]]	+	[[Category: Caldwell SJ]]
-	[[Category: Haydon~~, I C~~]]	+	[[Category: Haydon IC]]
-	[[Category: Hilvert, D]]	+	[[Category: Hilvert D]]
-	[[Category: Huang, P]]	+	[[Category: Huang P]]
-	[[Category: Zeymer, C]]	+	[[Category: Zeymer C]]
-	~~[[Category: De novo]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Ferredoxin fold]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Hyperstable]]~~	+
-	~~[[Category: Repeat protein]]~~	+
-	~~[[Category: Symmetric]]~~	+
-	~~[[Category: Symmetric fusion]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 08:13, 2 December 2020

OCA — Wed, 02 Dec 2020 08:13:01 GMT

←Older revision		Revision as of 08:13, 2 December 2020
Line 1:		Line 1:

	==De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE==		==De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE==
-	<StructureSection load='6wxo' size='340' side='right'caption='[[6wxo]]' scene=''>	+	<StructureSection load='6wxo' size='340' side='right'caption='[[6wxo]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WXO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WXO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wxo]] 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=6WXO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WXO FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wxo OCA], [http://pdbe.org/6wxo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wxo RCSB], [http://www.ebi.ac.uk/pdbsum/6wxo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wxo ProSAT]</span></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"><div style='overflow: auto; max-height: 3em;'>[[6wvs\|6wvs]], [[4pww\|4pww]], [[6wxp\|6wxp]]</div></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wxo OCA], [http://pdbe.org/6wxo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wxo RCSB], [http://www.ebi.ac.uk/pdbsum/6wxo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wxo ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	De novo protein design has succeeded in generating a large variety of globular proteins, but the construction of protein scaffolds with cavities that could accommodate large signaling molecules, cofactors, and substrates remains an outstanding challenge. The long, often flexible loops that form such cavities in many natural proteins are difficult to precisely program and thus challenging for computational protein design. Here we describe an alternative approach to this problem. We fused two stable proteins with C2 symmetry-a de novo designed dimeric ferredoxin fold and a de novo designed TIM barrel-such that their symmetry axes are aligned to create scaffolds with large cavities that can serve as binding pockets or enzymatic reaction chambers. The crystal structures of two such designs confirm the presence of a 420 cubic Angstrom chamber defined by the top of the designed TIM barrel and the bottom of the ferredoxin dimer. We functionalized the scaffold by installing a metal-binding site consisting of four glutamate residues close to the symmetry axis. The protein binds lanthanide ions with very high affinity as demonstrated by tryptophan-enhanced terbium luminescence. This approach can be extended to other metals and cofactors, making this scaffold a modular platform for the design of binding proteins and biocatalysts.
		+
		+	Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion.,Caldwell SJ, Haydon IC, Piperidou N, Huang PS, Bick MJ, Sjostrom HS, Hilvert D, Baker D, Zeymer C Proc Natl Acad Sci U S A. 2020 Nov 17. pii: 2008535117. doi:, 10.1073/pnas.2008535117. PMID:33203677<ref>PMID:33203677</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wxo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baker D]]	+	[[Category: Synthetic construct sequences]]
-	[[Category: Caldwell SJ]]	+	[[Category: Baker, D]]
-	[[Category: Haydon IC]]	+	[[Category: Caldwell, S J]]
-	[[Category: Hilvert D]]	+	[[Category: Haydon, I C]]
-	[[Category: Huang P]]	+	[[Category: Hilvert, D]]
-	[[Category: Zeymer C]]	+	[[Category: Huang, P]]
		+	[[Category: Zeymer, C]]
		+	[[Category: De novo]]
		+	[[Category: De novo protein]]
		+	[[Category: Ferredoxin fold]]
		+	[[Category: Homodimer]]
		+	[[Category: Hyperstable]]
		+	[[Category: Repeat protein]]
		+	[[Category: Symmetric]]
		+	[[Category: Symmetric fusion]]
		+	[[Category: Tim barrel]]

OCA at 06:54, 25 November 2020

OCA — Wed, 25 Nov 2020 06:54:51 GMT

←Older revision		Revision as of 06:54, 25 November 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6wxo is ON HOLD until Paper Publication~~	+	==De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE==
-		+	<StructureSection load='6wxo' size='340' side='right'caption='[[6wxo]]' scene=''>
-	~~Authors: Caldwell, S.J., Zeymer, C., Haydon, I.C., Huang, P., Hilvert, D., Baker, D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WXO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WXO FirstGlance]. <br>
-	~~Description:~~ De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wxo OCA], [http://pdbe.org/6wxo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wxo RCSB], [http://www.ebi.ac.uk/pdbsum/6wxo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wxo ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Haydon~~, I.C]]	+	__TOC__
-	[[Category: Baker, D]]	+	</StructureSection>
-	[[Category: Caldwell~~, S.J~~]]	+	[[Category: Large Structures]]
-	[[Category: Hilvert, D]]	+	[[Category: Baker D]]
-	[[Category: Huang, P]]	+	[[Category: Caldwell SJ]]
-	[[Category: Zeymer, C]]	+	[[Category: Haydon IC]]
		+	[[Category: Hilvert D]]
		+	[[Category: Huang P]]
		+	[[Category: Zeymer C]]

OCA at 08:34, 17 June 2020

OCA — Wed, 17 Jun 2020 08:34:36 GMT

←Older revision		Revision as of 08:34, 17 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6wxo is ON HOLD	+	The entry 6wxo is ON HOLD until Paper Publication

	Authors: Caldwell, S.J., Zeymer, C., Haydon, I.C., Huang, P., Hilvert, D., Baker, D.		Authors: Caldwell, S.J., Zeymer, C., Haydon, I.C., Huang, P., Hilvert, D., Baker, D.
Line 7:		Line 7:
	Description: De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE		Description: De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Haydon, I.C]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Caldwell, S.J]]		[[Category: Caldwell, S.J]]
Line 12:		Line 13:
	[[Category: Huang, P]]		[[Category: Huang, P]]
	[[Category: Zeymer, C]]		[[Category: Zeymer, C]]
-	[[Category: Haydon, I.C]]

OCA: Protected "6wxo" [edit=sysop:move=sysop]

OCA — Wed, 20 May 2020 04:20:00 GMT

Protected "6wxo" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:20, 20 May 2020

OCA: New page: '''Unreleased structure''' The entry 6wxo is ON HOLD Authors: Caldwell, S.J., Zeymer, C., Haydon, I.C., Huang, P., Hilvert, D., Baker, D. Description: De novo TIM barrel-ferredoxin fol...

OCA — Wed, 20 May 2020 04:19:59 GMT

New page: '''Unreleased structure''' The entry 6wxo is ON HOLD Authors: Caldwell, S.J., Zeymer, C., Haydon, I.C., Huang, P., Hilvert, D., Baker, D. Description: De novo TIM barrel-ferredoxin fol...

New page

'''Unreleased structure'''

The entry 6wxo is ON HOLD

Authors: Caldwell, S.J., Zeymer, C., Haydon, I.C., Huang, P., Hilvert, D., Baker, D.

Description: De novo TIM barrel-ferredoxin fold fusion homodimer with 2-histidine 2-glutamate centre TFD-HE
[[Category: Unreleased Structures]]
[[Category: Baker, D]]
[[Category: Caldwell, S.J]]
[[Category: Hilvert, D]]
[[Category: Huang, P]]
[[Category: Zeymer, C]]
[[Category: Haydon, I.C]]