1t6w - Revision history

OCA at 09:11, 22 May 2024

OCA — Wed, 22 May 2024 09:11:33 GMT

←Older revision		Revision as of 09:11, 22 May 2024
Line 20:		Line 20:
	</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=1t6w 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=1t6w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ca2+, "a signal of life and death", controls numerous cellular processes through interactions with proteins. An effective approach to understanding the role of Ca2+ is the design of a Ca2+-binding protein with predicted structural and functional properties. To design de novo Ca2+-binding sites in proteins is challenging due to the high coordination numbers and the incorporation of charged ligand residues, in addition to Ca2+-induced conformational change. Here, we demonstrate the successful design of a Ca2+-binding site in the non-Ca2+-binding cell adhesion protein CD2. This designed protein, Ca.CD2, exhibits selectivity for Ca2+ versus other di- and monovalent cations. In addition, La3+ (Kd 5.0 microM) and Tb3+ (Kd 6.6 microM) bind to the designed protein somewhat more tightly than does Ca2+ (Kd 1.4 mM). More interestingly, Ca.CD2 retains the native ability to associate with the natural target molecule. The solution structure reveals that Ca.CD2 binds Ca2+ at the intended site with the designed arrangement, which validates our general strategy for designing de novo Ca2+-binding proteins. The structural information also provides a close view of structural determinants that are necessary for a functional protein to accommodate the metal-binding site. This first success in designing Ca2+-binding proteins with desired structural and functional properties opens a new avenue in unveiling key determinants to Ca2+ binding, the mechanism of Ca2+ signaling, and Ca2+-dependent cell adhesion, while avoiding the complexities of the global conformational changes and cooperativity in natural Ca2+-binding proteins. It also represents a major achievement toward designing functional proteins controlled by Ca2+ binding.
		+
		+	Design of a calcium-binding protein with desired structure in a cell adhesion molecule.,Yang W, Wilkins AL, Ye Y, Liu ZR, Li SY, Urbauer JL, Hellinga HW, Kearney A, van der Merwe PA, Yang JJ J Am Chem Soc. 2005 Feb 23;127(7):2085-93. PMID:15713084<ref>PMID:15713084</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1t6w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:38, 1 May 2024

OCA — Wed, 01 May 2024 08:38:34 GMT

←Older revision		Revision as of 08:38, 1 May 2024
Line 1:		Line 1:

	==RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES==		==RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES==
-	<StructureSection load='1t6w' size='340' side='right'caption='[[1t6w~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1t6w' size='340' side='right'caption='[[1t6w]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [https://pdbe.org/1t6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [https://www.ebi.ac.uk/pdbsum/1t6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6w 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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [https://pdbe.org/1t6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [https://www.ebi.ac.uk/pdbsum/1t6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CD2_RAT CD2_RAT]] CD2 interacts with lymphocyte function-associated antigen (LFA-3) and CD48/BCM1 to mediate adhesion between T-cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function.	+	[https://www.uniprot.org/uniprot/CD2_RAT CD2_RAT] CD2 interacts with lymphocyte function-associated antigen (LFA-3) and CD48/BCM1 to mediate adhesion between T-cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=1t6w 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=1t6w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ca2+, "a signal of life and death", controls numerous cellular processes through interactions with proteins. An effective approach to understanding the role of Ca2+ is the design of a Ca2+-binding protein with predicted structural and functional properties. To design de novo Ca2+-binding sites in proteins is challenging due to the high coordination numbers and the incorporation of charged ligand residues, in addition to Ca2+-induced conformational change. Here, we demonstrate the successful design of a Ca2+-binding site in the non-Ca2+-binding cell adhesion protein CD2. This designed protein, Ca.CD2, exhibits selectivity for Ca2+ versus other di- and monovalent cations. In addition, La3+ (Kd 5.0 microM) and Tb3+ (Kd 6.6 microM) bind to the designed protein somewhat more tightly than does Ca2+ (Kd 1.4 mM). More interestingly, Ca.CD2 retains the native ability to associate with the natural target molecule. The solution structure reveals that Ca.CD2 binds Ca2+ at the intended site with the designed arrangement, which validates our general strategy for designing de novo Ca2+-binding proteins. The structural information also provides a close view of structural determinants that are necessary for a functional protein to accommodate the metal-binding site. This first success in designing Ca2+-binding proteins with desired structural and functional properties opens a new avenue in unveiling key determinants to Ca2+ binding, the mechanism of Ca2+ signaling, and Ca2+-dependent cell adhesion, while avoiding the complexities of the global conformational changes and cooperativity in natural Ca2+-binding proteins. It also represents a major achievement toward designing functional proteins controlled by Ca2+ binding.
-
-	Design of a calcium-binding protein with desired structure in a cell adhesion molecule.,Yang W, Wilkins AL, Ye Y, Liu ZR, Li SY, Urbauer JL, Hellinga HW, Kearney A, van der Merwe PA, Yang JJ J Am Chem Soc. 2005 Feb 23;127(7):2085-93. PMID:15713084<ref>PMID:15713084</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1t6w" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kearney, A~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Liu, Z R~~]]	+	[[Category: Kearney A]]
-	[[Category: ~~Merwe, P A.van der~~]]	+	[[Category: Liu Z-R]]
-	[[Category: Urbauer~~, J L~~]]	+	[[Category: Urbauer JL]]
-	[[Category: Wilkins~~, A L~~]]	+	[[Category: Wilkins AL]]
-	[[Category: Yang~~, J J~~]]	+	[[Category: Yang JJ]]
-	[[Category: Yang, W]]	+	[[Category: Yang W]]
-	[[Category: Ye, Y]]	+	[[Category: Ye Y]]
-	[[Category: ~~Calcium-binding protein]]~~	+	[[Category: Van der Merwe PA]]
-	~~[[Category: Cd2]]~~	+
-	~~[[Category: Design]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 09:23, 29 September 2021

OCA — Wed, 29 Sep 2021 09:23:35 GMT

←Older revision		Revision as of 09:23, 29 September 2021
Line 3:		Line 3:
	<StructureSection load='1t6w' size='340' side='right'caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1t6w' size='340' side='right'caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [~~http~~://pdbe.org/1t6w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t6w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6w 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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [https://pdbe.org/1t6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [https://www.ebi.ac.uk/pdbsum/1t6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CD2_RAT CD2_RAT]] CD2 interacts with lymphocyte function-associated antigen (LFA-3) and CD48/BCM1 to mediate adhesion between T-cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function.	+	[[https://www.uniprot.org/uniprot/CD2_RAT CD2_RAT]] CD2 interacts with lymphocyte function-associated antigen (LFA-3) and CD48/BCM1 to mediate adhesion between T-cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:14, 18 December 2019

OCA — Wed, 18 Dec 2019 14:14:45 GMT

←Older revision		Revision as of 14:14, 18 December 2019
Line 1:		Line 1:

	==RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES==		==RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES==
-	<StructureSection load='1t6w' size='340' side='right' caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1t6w' size='340' side='right'caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Kearney, A]]		[[Category: Kearney, A]]
	[[Category: Liu, Z R]]		[[Category: Liu, Z R]]

OCA at 07:54, 14 March 2018

OCA — Wed, 14 Mar 2018 07:54:50 GMT

←Older revision		Revision as of 07:54, 14 March 2018
Line 1:		Line 1:
		+
	==RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES==		==RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES==
	<StructureSection load='1t6w' size='340' side='right' caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1t6w' size='340' side='right' caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [http://pdbe.org/1t6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [http://www.ebi.ac.uk/pdbsum/1t6w 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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [http://pdbe.org/1t6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [http://www.ebi.ac.uk/pdbsum/1t6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6w 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/t6/1t6w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6w_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>
	</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=1t6w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:24, 11 September 2015

OCA — Fri, 11 Sep 2015 09:24:37 GMT

←Older revision		Revision as of 09:24, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1t6w' size='340' side='right' caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1t6w' size='340' side='right' caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [http://www.ebi.ac.uk/pdbsum/1t6w 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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [http://pdbe.org/1t6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [http://www.ebi.ac.uk/pdbsum/1t6w 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 1t6w" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Kearney, A]]		[[Category: Kearney, A]]
	[[Category: Liu, Z R]]		[[Category: Liu, Z R]]

OCA at 14:28, 25 December 2014

OCA — Thu, 25 Dec 2014 14:28:10 GMT

←Older revision		Revision as of 14:28, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [http://www.ebi.ac.uk/pdbsum/1t6w 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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [http://www.ebi.ac.uk/pdbsum/1t6w PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CD2_RAT CD2_RAT]] CD2 interacts with lymphocyte function-associated antigen (LFA-3) and CD48/BCM1 to mediate adhesion between T-cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Kearney, A.]]	+	[[Category: Kearney, A]]
-	[[Category: Liu, Z R.]]	+	[[Category: Liu, Z R]]
-	[[Category: Merwe, P A.van der.]]	+	[[Category: Merwe, P A.van der]]
-	[[Category: Urbauer, J L.]]	+	[[Category: Urbauer, J L]]
-	[[Category: Wilkins, A L.]]	+	[[Category: Wilkins, A L]]
-	[[Category: Yang, J J.]]	+	[[Category: Yang, J J]]
-	[[Category: Yang, W.]]	+	[[Category: Yang, W]]
-	[[Category: Ye, Y.]]	+	[[Category: Ye, Y]]
	[[Category: Calcium-binding protein]]		[[Category: Calcium-binding protein]]
	[[Category: Cd2]]		[[Category: Cd2]]
	[[Category: Design]]		[[Category: Design]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]

OCA at 21:34, 29 September 2014

OCA — Mon, 29 Sep 2014 21:34:12 GMT

←Older revision		Revision as of 21:34, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1t6w.~~png\|left~~\|200px]]	+	==RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES==
		+	<StructureSection load='1t6w' size='340' side='right' caption='[[1t6w]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<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=1t6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6w RCSB], [http://www.ebi.ac.uk/pdbsum/1t6w 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/t6/1t6w_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 ==
		+	Ca2+, "a signal of life and death", controls numerous cellular processes through interactions with proteins. An effective approach to understanding the role of Ca2+ is the design of a Ca2+-binding protein with predicted structural and functional properties. To design de novo Ca2+-binding sites in proteins is challenging due to the high coordination numbers and the incorporation of charged ligand residues, in addition to Ca2+-induced conformational change. Here, we demonstrate the successful design of a Ca2+-binding site in the non-Ca2+-binding cell adhesion protein CD2. This designed protein, Ca.CD2, exhibits selectivity for Ca2+ versus other di- and monovalent cations. In addition, La3+ (Kd 5.0 microM) and Tb3+ (Kd 6.6 microM) bind to the designed protein somewhat more tightly than does Ca2+ (Kd 1.4 mM). More interestingly, Ca.CD2 retains the native ability to associate with the natural target molecule. The solution structure reveals that Ca.CD2 binds Ca2+ at the intended site with the designed arrangement, which validates our general strategy for designing de novo Ca2+-binding proteins. The structural information also provides a close view of structural determinants that are necessary for a functional protein to accommodate the metal-binding site. This first success in designing Ca2+-binding proteins with desired structural and functional properties opens a new avenue in unveiling key determinants to Ca2+ binding, the mechanism of Ca2+ signaling, and Ca2+-dependent cell adhesion, while avoiding the complexities of the global conformational changes and cooperativity in natural Ca2+-binding proteins. It also represents a major achievement toward designing functional proteins controlled by Ca2+ binding.

-	~~{{STRUCTURE_1t6w\| PDB=1t6w \| SCENE= }}~~	+	Design of a calcium-binding protein with desired structure in a cell adhesion molecule.,Yang W, Wilkins AL, Ye Y, Liu ZR, Li SY, Urbauer JL, Hellinga HW, Kearney A, van der Merwe PA, Yang JJ J Am Chem Soc. 2005 Feb 23;127(7):2085-93. PMID:15713084<ref>PMID:15713084</ref>

-	~~===RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR~~, ~~20 STRUCTURES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15713084}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1t6w]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015713084<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Kearney, A.]]		[[Category: Kearney, A.]]

OCA: Protected "1t6w" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:53:26 GMT

Protected "1t6w" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:53, 5 January 2013

OCA at 12:53, 5 January 2013

OCA — Sat, 05 Jan 2013 12:53:23 GMT

←Older revision		Revision as of 12:53, 5 January 2013
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-	{{Seed}}
	[[Image:1t6w.png\|left\|200px]]		[[Image:1t6w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t6w", 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_1t6w\| PDB=1t6w \| SCENE= }}		{{STRUCTURE_1t6w\| PDB=1t6w \| SCENE= }}

	===RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES===		===RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15713084}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15713084 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15713084}}		{{ABSTRACT_PUBMED_15713084}}

	==About this Structure==		==About this Structure==
-	~~1T6W~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA].	+	[[1t6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6W OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15713084~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015713084</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Kearney, A.]]		[[Category: Kearney, A.]]
Line 36:		Line 24:
	[[Category: Cd2]]		[[Category: Cd2]]
	[[Category: Design]]		[[Category: Design]]
-	[[Category: ~~Nmr~~]]	+	[[Category: Metal binding protein]]
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:42:14 2009''~~	+