2qbw - Revision history

OCA at 09:15, 21 February 2024

OCA — Wed, 21 Feb 2024 09:15:10 GMT

←Older revision		Revision as of 09:15, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2qbw' size='340' side='right'caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2qbw' size='340' side='right'caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qbw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qbw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBW FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ERBB2IP (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</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]] 1.8Å</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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [https://pdbe.org/2qbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [https://www.ebi.ac.uk/pdbsum/2qbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbw 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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [https://pdbe.org/2qbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [https://www.ebi.ac.uk/pdbsum/2qbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~LAP2_HUMAN LAP2_HUMAN]~~] Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state.<ref>PMID:10878805</ref>	+	[https://www.uniprot.org/uniprot/ERBIN_HUMAN ERBIN_HUMAN] Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state (PubMed:16203728). Inhibits NOD2-dependent NF-kappa-B signaling and proinflammatory cytokine secretion (PubMed:16203728).<ref>PMID:10878805</ref> <ref>PMID:16203728</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qbw ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qbw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Most natural proteins performing sophisticated tasks contain multiple domains where an active site is located at the domain interface. Comparative structural analyses suggest that major leaps in protein function occur through gene recombination events that connect two or more protein domains to generate a new active site, frequently occurring at the newly created domain interface. However, such functional leaps by combination of unrelated domains have not been directly demonstrated. Here we show that highly specific and complex protein functions can be generated by joining a low-affinity peptide-binding domain with a functionally inert second domain and subsequently optimizing the domain interface. These directed evolution processes dramatically enhanced both affinity and specificity to a level unattainable with a single domain, corresponding to >500-fold and >2,000-fold increases of affinity and specificity, respectively. An x-ray crystal structure revealed that the resulting "affinity clamp" had clamshell architecture as designed, with large additional binding surface contributed by the second domain. The affinity clamps having a single-nanomolar dissociation constant outperformed a monoclonal antibody in immunochemical applications. This work establishes evolutionary paths from isolated domains with primitive function to multidomain proteins with sophisticated function and introduces a new protein-engineering concept that allows for the generation of highly functional affinity reagents to a predefined target. The prevalence and variety of natural interaction domains suggest that numerous new functions can be designed by using directed domain interface evolution.
-
-	Design of protein function leaps by directed domain interface evolution.,Huang J, Koide A, Makabe K, Koide S Proc Natl Acad Sci U S A. 2008 May 6;105(18):6578-83. Epub 2008 Apr 29. PMID:18445649<ref>PMID:18445649</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2qbw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Huang, J]]	+	[[Category: Huang J]]
-	[[Category: Koide, A]]	+	[[Category: Koide A]]
-	[[Category: Koide, S]]	+	[[Category: Koide S]]
-	[[Category: Makabe, K]]	+	[[Category: Makabe K]]
-	~~[[Category: Fibronectin pdz]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 08:14, 25 June 2021

OCA — Fri, 25 Jun 2021 08:14:55 GMT

←Older revision		Revision as of 08:14, 25 June 2021
Line 1:		Line 1:

	==The crystal structure of PDZ-Fibronectin fusion protein==		==The crystal structure of PDZ-Fibronectin fusion protein==
-	<StructureSection load='2qbw' size='340' side='right' caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2qbw' size='340' side='right'caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qbw]] 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=2QBW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qbw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBW FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([https://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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [~~http~~://pdbe.org/2qbw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qbw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbw 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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [https://pdbe.org/2qbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [https://www.ebi.ac.uk/pdbsum/2qbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LAP2_HUMAN LAP2_HUMAN]] Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state.<ref>PMID:10878805</ref>	+	[[https://www.uniprot.org/uniprot/LAP2_HUMAN LAP2_HUMAN]] Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state.<ref>PMID:10878805</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Fibronectin\|Fibronectin]]	+	*[[Fibronectin 3D structures\|Fibronectin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Huang, J]]		[[Category: Huang, J]]
	[[Category: Koide, A]]		[[Category: Koide, A]]

OCA at 08:56, 29 August 2018

OCA — Wed, 29 Aug 2018 08:56:43 GMT

←Older revision		Revision as of 08:56, 29 August 2018
Line 1:		Line 1:
		+
	==The crystal structure of PDZ-Fibronectin fusion protein==		==The crystal structure of PDZ-Fibronectin fusion protein==
	<StructureSection load='2qbw' size='340' side='right' caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2qbw' size='340' side='right' caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2qbw]] 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=2QBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBW FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qbw]] 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=2QBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBW FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [http://pdbe.org/2qbw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [http://www.ebi.ac.uk/pdbsum/2qbw 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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [http://pdbe.org/2qbw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [http://www.ebi.ac.uk/pdbsum/2qbw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/2qbw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/2qbw_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 06:45, 8 February 2016

OCA — Mon, 08 Feb 2016 06:45:10 GMT

←Older revision		Revision as of 06:45, 8 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qbw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:55, 10 September 2015

OCA — Thu, 10 Sep 2015 08:55:39 GMT

←Older revision		Revision as of 08:55, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2qbw' size='340' side='right' caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2qbw' size='340' side='right' caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qbw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qbw]] 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=2QBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBW FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [http://www.ebi.ac.uk/pdbsum/2qbw 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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [http://pdbe.org/2qbw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [http://www.ebi.ac.uk/pdbsum/2qbw PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 2qbw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Huang, J]]		[[Category: Huang, J]]
	[[Category: Koide, A]]		[[Category: Koide, A]]

OCA at 21:24, 24 December 2014

OCA — Wed, 24 Dec 2014 21:24:08 GMT

←Older revision		Revision as of 21:24, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qbw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBW FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qbw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [http://www.ebi.ac.uk/pdbsum/2qbw 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=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [http://www.ebi.ac.uk/pdbsum/2qbw PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LAP2_HUMAN LAP2_HUMAN]] Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state.<ref>PMID:10878805</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Huang, J.]]	+	[[Category: Huang, J]]
-	[[Category: Koide, A.]]	+	[[Category: Koide, A]]
-	[[Category: Koide, S.]]	+	[[Category: Koide, S]]
-	[[Category: Makabe, K.]]	+	[[Category: Makabe, K]]
	[[Category: Fibronectin pdz]]		[[Category: Fibronectin pdz]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 09:17, 29 September 2014

OCA — Mon, 29 Sep 2014 09:17:03 GMT

←Older revision		Revision as of 09:17, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2qbw.~~png\|left~~\|200px]]	+	==The crystal structure of PDZ-Fibronectin fusion protein==
		+	<StructureSection load='2qbw' size='340' side='right' caption='[[2qbw]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qbw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2IP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbw RCSB], [http://www.ebi.ac.uk/pdbsum/2qbw PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/2qbw_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most natural proteins performing sophisticated tasks contain multiple domains where an active site is located at the domain interface. Comparative structural analyses suggest that major leaps in protein function occur through gene recombination events that connect two or more protein domains to generate a new active site, frequently occurring at the newly created domain interface. However, such functional leaps by combination of unrelated domains have not been directly demonstrated. Here we show that highly specific and complex protein functions can be generated by joining a low-affinity peptide-binding domain with a functionally inert second domain and subsequently optimizing the domain interface. These directed evolution processes dramatically enhanced both affinity and specificity to a level unattainable with a single domain, corresponding to >500-fold and >2,000-fold increases of affinity and specificity, respectively. An x-ray crystal structure revealed that the resulting "affinity clamp" had clamshell architecture as designed, with large additional binding surface contributed by the second domain. The affinity clamps having a single-nanomolar dissociation constant outperformed a monoclonal antibody in immunochemical applications. This work establishes evolutionary paths from isolated domains with primitive function to multidomain proteins with sophisticated function and introduces a new protein-engineering concept that allows for the generation of highly functional affinity reagents to a predefined target. The prevalence and variety of natural interaction domains suggest that numerous new functions can be designed by using directed domain interface evolution.

-	~~{{STRUCTURE_2qbw\| PDB=2qbw \| SCENE= }}~~	+	Design of protein function leaps by directed domain interface evolution.,Huang J, Koide A, Makabe K, Koide S Proc Natl Acad Sci U S A. 2008 May 6;105(18):6578-83. Epub 2008 Apr 29. PMID:18445649<ref>PMID:18445649</ref>

-	~~===The crystal structure~~ of ~~PDZ-Fibronectin fusion protein===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18445649}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2qbw]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA].~~	+

	==See Also==		==See Also==
	*[[Fibronectin\|Fibronectin]]		*[[Fibronectin\|Fibronectin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018445649<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Huang, J.]]		[[Category: Huang, J.]]

OCA at 09:16, 20 October 2012

OCA — Sat, 20 Oct 2012 09:16:57 GMT

←Older revision		Revision as of 09:16, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2qbw]] is a 2 chain structure ~~of [[Fibronectin]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA].	+	[[2qbw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA].

	==See Also==		==See Also==

OCA: Protected "2qbw" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 22:20:07 GMT

Protected "2qbw" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:20, 25 July 2012

OCA at 22:20, 25 July 2012

OCA — Wed, 25 Jul 2012 22:20:06 GMT

←Older revision		Revision as of 22:20, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2qbw.png\|left\|200px]]		[[Image:2qbw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qbw", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2qbw\| PDB=2qbw \| SCENE= }}		{{STRUCTURE_2qbw\| PDB=2qbw \| SCENE= }}

	===The crystal structure of PDZ-Fibronectin fusion protein===		===The crystal structure of PDZ-Fibronectin fusion protein===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18445649}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18445649 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18445649}}		{{ABSTRACT_PUBMED_18445649}}

	==About this Structure==		==About this Structure==
-	~~2QBW~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA].	+	[[2qbw]] is a 2 chain structure of [[Fibronectin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBW OCA].
		+
		+	==See Also==
		+	*[[Fibronectin\|Fibronectin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18445649~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018445649</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Huang, J.]]		[[Category: Huang, J.]]
Line 31:		Line 22:
	[[Category: Fibronectin pdz]]		[[Category: Fibronectin pdz]]
	[[Category: Unknown function]]		[[Category: Unknown function]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:54:54 2009''