5j0k - Revision history

OCA at 12:36, 6 March 2024

OCA — Wed, 06 Mar 2024 12:36:06 GMT

←Older revision		Revision as of 12:36, 6 March 2024
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [https://pdbe.org/5j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [https://www.ebi.ac.uk/pdbsum/5j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0k 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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [https://pdbe.org/5j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [https://www.ebi.ac.uk/pdbsum/5j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0k ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.
-
-	De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.,Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D Science. 2016 May 6;352(6286):680-7. doi: 10.1126/science.aad8865. PMID:27151862<ref>PMID:27151862</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5j0k" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:41, 6 September 2023

OCA — Wed, 06 Sep 2023 10:41:10 GMT

←Older revision		Revision as of 10:41, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5j0k' size='340' side='right'caption='[[5j0k]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='5j0k' size='340' side='right'caption='[[5j0k]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j0k]] 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=5J0K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j0k]] 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=5J0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J0K 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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [~~http~~://pdbe.org/5j0k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j0k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0k 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]] 1.54Å</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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [https://pdbe.org/5j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [https://www.ebi.ac.uk/pdbsum/5j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Boyken, S]]	+	[[Category: Boyken S]]
-	[[Category: Chen, Z]]	+	[[Category: Chen Z]]
-	[[Category: DiMaio, F]]	+	[[Category: DiMaio F]]
-	[[Category: Ford, A]]	+	[[Category: Ford A]]
-	[[Category: Gilmore, J]]	+	[[Category: Gilmore J]]
-	[[Category: Groves, B]]	+	[[Category: Groves B]]
-	[[Category: Langan~~, R A~~]]	+	[[Category: Langan RA]]
-	[[Category: Oberdorfer, G]]	+	[[Category: Oberdorfer G]]
-	[[Category: Pereira~~, J H~~]]	+	[[Category: Pereira JH]]
-	[[Category: Sankaran, B]]	+	[[Category: Sankaran B]]
-	[[Category: Seelig, G]]	+	[[Category: Seelig G]]
-	[[Category: Xu, C]]	+	[[Category: Xu C]]
-	[[Category: Zwart~~, P H]]~~	+	[[Category: Zwart PH]]
-	~~[[Category: De novo design]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Rosetta~~]]	+

OCA at 07:23, 10 June 2020

OCA — Wed, 10 Jun 2020 07:23:38 GMT

←Older revision		Revision as of 07:23, 10 June 2020
Line 1:		Line 1:

	==De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity==		==De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity==
-	<StructureSection load='5j0k' size='340' side='right' caption='[[5j0k]], [[Resolution\|resolution]] 1.54Å' scene=''>	+	<StructureSection load='5j0k' size='340' side='right'caption='[[5j0k]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j0k]] 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=5J0K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j0k]] 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=5J0K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J0K 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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [http://pdbe.org/5j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [http://www.ebi.ac.uk/pdbsum/5j0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0k ProSAT]</span></td></tr>	+	</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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [http://pdbe.org/5j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [http://www.ebi.ac.uk/pdbsum/5j0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]

OCA at 06:19, 1 November 2017

OCA — Wed, 01 Nov 2017 06:19:37 GMT

←Older revision		Revision as of 06:19, 1 November 2017
Line 3:		Line 3:
	<StructureSection load='5j0k' size='340' side='right' caption='[[5j0k]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='5j0k' size='340' side='right' caption='[[5j0k]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j0k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j0k]] 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=5J0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J0K 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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [http://pdbe.org/5j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [http://www.ebi.ac.uk/pdbsum/5j0k 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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [http://pdbe.org/5j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [http://www.ebi.ac.uk/pdbsum/5j0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Boyken, S]]		[[Category: Boyken, S]]

OCA at 23:03, 1 June 2016

OCA — Wed, 01 Jun 2016 23:03:03 GMT

←Older revision		Revision as of 23:03, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j0k is ~~ON HOLD until Paper~~ Publication	+	==De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity==
		+	<StructureSection load='5j0k' size='340' side='right' caption='[[5j0k]], [[Resolution\|resolution]] 1.54Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5j0k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J0K 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=5j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0k OCA], [http://pdbe.org/5j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0k RCSB], [http://www.ebi.ac.uk/pdbsum/5j0k PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.

-	~~Authors: Sankaran, B., Zwart, P.H., Pereira, J.H., Baker, D~~., Boyken~~, S.~~, Chen, Z., Groves, B., Langan~~, R.A.~~, Oberdorfer, G., Ford, A., Gilmore~~, J.~~, Xu, C., DiMaio, F., Seelig, G.	+	De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.,Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D Science. 2016 May 6;352(6286):680-7. doi: 10.1126/science.aad8865. PMID:27151862<ref>PMID:27151862</ref>

-	~~Description: De novo design~~ of ~~protein homo~~-~~oligomers with modular hydrogen bond network~~-~~mediated specificity~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Pereira~~, ~~J.H~~]]	+	<div class="pdbe-citations 5j0k" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Gilmore~~, J]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Baker, D]]
		+	[[Category: Boyken, S]]
		+	[[Category: Chen, Z]]
		+	[[Category: DiMaio, F]]
	[[Category: Ford, A]]		[[Category: Ford, A]]
		+	[[Category: Gilmore, J]]
	[[Category: Groves, B]]		[[Category: Groves, B]]
		+	[[Category: Langan, R A]]
	[[Category: Oberdorfer, G]]		[[Category: Oberdorfer, G]]
		+	[[Category: Pereira, J H]]
	[[Category: Sankaran, B]]		[[Category: Sankaran, B]]
-	[[Category: Chen, Z]]
	[[Category: Seelig, G]]		[[Category: Seelig, G]]
-	[[Category: Baker, D]]
-	[[Category: Boyken, S]]
	[[Category: Xu, C]]		[[Category: Xu, C]]
-	[[Category: ~~Dimaio~~, F]]	+	[[Category: Zwart, P H]]
-	[[Category: ~~Langan, R.A~~]]	+	[[Category: De novo design]]
-	[[Category: ~~Zwart, P.H~~]]	+	[[Category: De novo protein]]
		+	[[Category: Rosetta]]

OCA at 14:56, 15 May 2016

OCA — Sun, 15 May 2016 14:56:17 GMT

←Older revision		Revision as of 14:56, 15 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j0k is ON HOLD	+	The entry 5j0k is ON HOLD until Paper Publication

	Authors: Sankaran, B., Zwart, P.H., Pereira, J.H., Baker, D., Boyken, S., Chen, Z., Groves, B., Langan, R.A., Oberdorfer, G., Ford, A., Gilmore, J., Xu, C., DiMaio, F., Seelig, G.		Authors: Sankaran, B., Zwart, P.H., Pereira, J.H., Baker, D., Boyken, S., Chen, Z., Groves, B., Langan, R.A., Oberdorfer, G., Ford, A., Gilmore, J., Xu, C., DiMaio, F., Seelig, G.

OCA: Protected "5j0k" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:15:43 GMT

Protected "5j0k" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:15, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j0k is ON HOLD Authors: Sankaran, B., Zwart, P.H., Pereira, J.H., Baker, D., Boyken, S., Chen, Z., Groves, B., Langan, R.A., Oberdorfer, G., Ford, ...

OCA — Wed, 11 May 2016 01:15:41 GMT

New page: '''Unreleased structure''' The entry 5j0k is ON HOLD Authors: Sankaran, B., Zwart, P.H., Pereira, J.H., Baker, D., Boyken, S., Chen, Z., Groves, B., Langan, R.A., Oberdorfer, G., Ford, ...

New page

'''Unreleased structure'''

The entry 5j0k is ON HOLD

Authors: Sankaran, B., Zwart, P.H., Pereira, J.H., Baker, D., Boyken, S., Chen, Z., Groves, B., Langan, R.A., Oberdorfer, G., Ford, A., Gilmore, J., Xu, C., DiMaio, F., Seelig, G.

Description: De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
[[Category: Unreleased Structures]]
[[Category: Pereira, J.H]]
[[Category: Gilmore, J]]
[[Category: Ford, A]]
[[Category: Groves, B]]
[[Category: Oberdorfer, G]]
[[Category: Sankaran, B]]
[[Category: Chen, Z]]
[[Category: Seelig, G]]
[[Category: Baker, D]]
[[Category: Boyken, S]]
[[Category: Xu, C]]
[[Category: Dimaio, F]]
[[Category: Langan, R.A]]
[[Category: Zwart, P.H]]