5ucl - Revision history

OCA: Redirecting to 6njg

OCA — Wed, 06 Mar 2019 07:17:52 GMT

Redirecting to 6njg

←Older revision		Revision as of 07:17, 6 March 2019
Line 1:		Line 1:
-		+	#REDIRECT [[6njg]] This PDB entry is obsolete and replaced by 6njg
-	~~==Ubiquitin Variant in Complex with Binding Partner==~~	+
-	~~<StructureSection load='5ucl' size='340' side='right' caption='~~[[~~5ucl]], [[Resolution\|resolution]] 2.35Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[5ucl~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UCL FirstGlance]. <br>	+
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ucl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ucl OCA], [http://pdbe.org/5ucl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ucl RCSB], [http://www.ebi.ac.uk/pdbsum/5ucl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ucl ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	~~[[http://www.uniprot.org/uniprot/VPS27_YEAST VPS27_YEAST]] Component of the ESCRT-0 complex which is the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB)~~ and recruits ESCRT-I to the MVB outer membrane. Controls exit from the prevacuolar compartment (PVC) in both the forward direction to the vacuole and the return to the Golgi. Allows VPS10 to return to the (trans-Golgi network) TGN from the PVC. Might also function as an alternate adapter in the COPIb clathrin-like coat.<ref>PMID:3062374</ref> <ref>PMID:1493335</ref> <ref>PMID:8649377</ref> <ref>PMID:9015300</ref> <ref>PMID:9265642</ref> <ref>PMID:11208109</ref> <ref>PMID:11416128</ref> <ref>PMID:12055639</ref> <ref>PMID:11872141</ref> <ref>PMID:12900393</ref> <ref>PMID:14581452</ref> <ref>PMID:15166140</ref> <ref>PMID:15107463</ref> <ref>PMID:15086794</ref> <ref>PMID:17101773</ref> <ref>PMID:17135292</ref>	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ubiquitin interacting motifs (UIMs) are short alpha-helices found in a number of eukaryotic proteins. UIMs interact weakly but specifically with ubiquitin conjugated to other proteins, and in so doing, mediate specific cellular signals. Here we used phage display to generate ubiquitin variants (UbVs) targeting the N-terminal UIM of the yeast Vps27 protein. Selections yielded UbV.v27.1, which recognized the cognate UIM with high specificity relative to other yeast UIMs and bound with an affinity more than two orders of magnitude higher than that of ubiquitin. Structural and mutational studies of the UbV.v27.1-UIM complex revealed the molecular details for the enhanced affinity and specificity of UbV.v27.1, and underscored the importance of changes at the binding interface as well as at positions that do not contact the UIM. Our study highlights the power of the phage display approach for selecting UbVs with unprecedented affinity and high selectivity for particular alpha-helical UIM domains within proteomes, and it establishes a general approach for the development of inhibitors targeting interactions of this type. This article is protected by ~~copyright. All rights reserved.~~	+
-		+
-	Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif.,Manczyk N, Yates BP, Veggiani G, Ernst A, Sicheri F, Sidhu SS Protein Sci. 2017 Mar 9. doi: 10.1002/pro.3155. PMID:28276594<ref>PMID:28276594</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5ucl" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Human]]~~	+
-	~~[[Category: Manczyk, N]]~~	+
-	~~[[Category: Sicheri, F]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Ubiquitin variant]]~~	+
-	~~[[Category: Uim]]~~	+

OCA at 14:33, 6 November 2017

OCA — Mon, 06 Nov 2017 14:33:00 GMT

←Older revision		Revision as of 14:33, 6 November 2017
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	<StructureSection load='5ucl' size='340' side='right' caption='[[5ucl]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='5ucl' size='340' side='right' caption='[[5ucl]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ucl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ucl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UCL 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=5ucl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ucl OCA], [http://pdbe.org/5ucl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ucl RCSB], [http://www.ebi.ac.uk/pdbsum/5ucl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ucl ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ucl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ucl OCA], [http://pdbe.org/5ucl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ucl RCSB], [http://www.ebi.ac.uk/pdbsum/5ucl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ucl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Manczyk, N]]		[[Category: Manczyk, N]]
	[[Category: Sicheri, F]]		[[Category: Sicheri, F]]

OCA at 16:14, 22 March 2017

OCA — Wed, 22 Mar 2017 16:14:52 GMT

←Older revision		Revision as of 16:14, 22 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5ucl is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Ubiquitin Variant in Complex with Binding Partner==
		+	<StructureSection load='5ucl' size='340' side='right' caption='[[5ucl]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ucl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UCL 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=5ucl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ucl OCA], [http://pdbe.org/5ucl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ucl RCSB], [http://www.ebi.ac.uk/pdbsum/5ucl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ucl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VPS27_YEAST VPS27_YEAST]] Component of the ESCRT-0 complex which is the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB) and recruits ESCRT-I to the MVB outer membrane. Controls exit from the prevacuolar compartment (PVC) in both the forward direction to the vacuole and the return to the Golgi. Allows VPS10 to return to the (trans-Golgi network) TGN from the PVC. Might also function as an alternate adapter in the COPIb clathrin-like coat.<ref>PMID:3062374</ref> <ref>PMID:1493335</ref> <ref>PMID:8649377</ref> <ref>PMID:9015300</ref> <ref>PMID:9265642</ref> <ref>PMID:11208109</ref> <ref>PMID:11416128</ref> <ref>PMID:12055639</ref> <ref>PMID:11872141</ref> <ref>PMID:12900393</ref> <ref>PMID:14581452</ref> <ref>PMID:15166140</ref> <ref>PMID:15107463</ref> <ref>PMID:15086794</ref> <ref>PMID:17101773</ref> <ref>PMID:17135292</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitin interacting motifs (UIMs) are short alpha-helices found in a number of eukaryotic proteins. UIMs interact weakly but specifically with ubiquitin conjugated to other proteins, and in so doing, mediate specific cellular signals. Here we used phage display to generate ubiquitin variants (UbVs) targeting the N-terminal UIM of the yeast Vps27 protein. Selections yielded UbV.v27.1, which recognized the cognate UIM with high specificity relative to other yeast UIMs and bound with an affinity more than two orders of magnitude higher than that of ubiquitin. Structural and mutational studies of the UbV.v27.1-UIM complex revealed the molecular details for the enhanced affinity and specificity of UbV.v27.1, and underscored the importance of changes at the binding interface as well as at positions that do not contact the UIM. Our study highlights the power of the phage display approach for selecting UbVs with unprecedented affinity and high selectivity for particular alpha-helical UIM domains within proteomes, and it establishes a general approach for the development of inhibitors targeting interactions of this type. This article is protected by copyright. All rights reserved.

-	~~Authors~~:	+	Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif.,Manczyk N, Yates BP, Veggiani G, Ernst A, Sicheri F, Sidhu SS Protein Sci. 2017 Mar 9. doi: 10.1002/pro.3155. PMID:28276594<ref>PMID:28276594</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ucl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Manczyk, N]]
		+	[[Category: Sicheri, F]]
		+	[[Category: Protein binding]]
		+	[[Category: Ubiquitin variant]]
		+	[[Category: Uim]]

OCA at 16:29, 1 February 2017

OCA — Wed, 01 Feb 2017 16:29:21 GMT

←Older revision		Revision as of 16:29, 1 February 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 04 Jan 2017 15:40:04 GMT

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

←Older revision

Revision as of 15:40, 4 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ucl is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Jan 2017 15:40:03 GMT

New page: '''Unreleased structure''' The entry 5ucl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ucl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]