2ci9 - Revision history

OCA at 06:38, 1 May 2024

OCA — Wed, 01 May 2024 06:38:59 GMT

←Older revision		Revision as of 06:38, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='2ci9' size='340' side='right'caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2ci9' size='340' side='right'caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ci9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=PTR:O~~-~~PHOSPHOTYROSINE'>PTR</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]] 1.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [https://pdbe.org/2ci9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ci9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ci9 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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [https://pdbe.org/2ci9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ci9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ci9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref> [[https://www.uniprot.org/uniprot/TIR_ECO27 TIR_ECO27]] Multifunctional protein that is required for efficient pedestal formation in host epithelial cells during infection. The extracellular region acts as a receptor for bacterial intimin, allowing the bacterium to attach tightly to the host-cell surface. Simultaneously, the intracellular region initiates a signaling cascade in the host cell, which leads to actin polymerization and formation of actin pedestals at the sites of bacterial adhesion. In strain E2348/69, acts mainly via the host adaptor proteins NCK1 and NCK2. Once clustered and phosphorylated at Tyr-474, Tir binds to NCK proteins, which in turn bind and activate host WASL/N-WASP, leading to actin polymerization. Can also trigger an inefficient, NCK-independent pedestal formation. This pathway involves phosphorylation of Tyr-454 and probably a putative host adaptor. Acts also via direct binding to the host cytoskeletal protein alpha-actinin in a NCK- and phosphotyrosine-independent manner. This interaction may stabilize the pedestal, but is not essential for its formation.<ref>PMID:10096089</ref> <ref>PMID:14757753</ref> <ref>PMID:14764108</ref> <ref>PMID:15813734</ref> <ref>PMID:17521329</ref> <ref>PMID:9390560</ref>	+	[https://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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=2ci9 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=2ci9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nck proteins are essential Src homology (SH) 2 and SH3 domain-bearing adapters that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. Two mammalian pathogens, enteropathogenic Escherichia coli and vaccinia virus, exploit Nck as part of their infection strategy. Conflicting data indicate potential differences in the recognition specificities of the SH2 domains of the isoproteins Nck1 (Nckalpha) and Nck2 (Nckbeta and Grb4). We have characterized the binding specificities of both SH2 domains and find them to be essentially indistinguishable. Crystal structures of both domains in complex with phosphopeptides derived from the enteropathogenic E. coli protein Tir concur in identifying highly conserved, specific recognition of the phosphopeptide. Differential peptide recognition can therefore not account for the preference of either Nck in particular signaling pathways. Binding studies using sequentially mutated, high affinity phosphopeptides establish the sequence variability tolerated in peptide recognition. Based on this binding motif, we identify potential new binding partners of Nck1 and Nck2 and confirm this experimentally for the Arf-GAP GIT1.
-
-	The phosphotyrosine peptide binding specificity of Nck1 and Nck2 Src homology 2 domains.,Frese S, Schubert WD, Findeis AC, Marquardt T, Roske YS, Stradal TE, Heinz DW J Biol Chem. 2006 Jun 30;281(26):18236-45. Epub 2006 Apr 24. PMID:16636066<ref>PMID:16636066</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2ci9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Escherichia coli]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Findeis~~, A C~~]]	+	[[Category: Findeis AC]]
-	[[Category: Frese, S]]	+	[[Category: Frese S]]
-	[[Category: Heinz~~, D W~~]]	+	[[Category: Heinz DW]]
-	[[Category: Marquardt, T]]	+	[[Category: Marquardt T]]
-	[[Category: Roske~~, Y S~~]]	+	[[Category: Roske YS]]
-	[[Category: Schubert, W D]]	+	[[Category: Schubert W-D]]
-	[[Category: Stradal~~, T E.B]]~~	+	[[Category: Stradal TEB]]
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Protein-binding]]~~	+
-	~~[[Category: Sh2-domain-complex~~]]	+

OCA at 07:12, 24 February 2021

OCA — Wed, 24 Feb 2021 07:12:04 GMT

←Older revision		Revision as of 07:12, 24 February 2021
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	<StructureSection load='2ci9' size='340' side='right'caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2ci9' size='340' side='right'caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</div></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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [~~http~~://pdbe.org/2ci9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ci9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ci9 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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [https://pdbe.org/2ci9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ci9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ci9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref> [[~~http~~://www.uniprot.org/uniprot/TIR_ECO27 TIR_ECO27]] Multifunctional protein that is required for efficient pedestal formation in host epithelial cells during infection. The extracellular region acts as a receptor for bacterial intimin, allowing the bacterium to attach tightly to the host-cell surface. Simultaneously, the intracellular region initiates a signaling cascade in the host cell, which leads to actin polymerization and formation of actin pedestals at the sites of bacterial adhesion. In strain E2348/69, acts mainly via the host adaptor proteins NCK1 and NCK2. Once clustered and phosphorylated at Tyr-474, Tir binds to NCK proteins, which in turn bind and activate host WASL/N-WASP, leading to actin polymerization. Can also trigger an inefficient, NCK-independent pedestal formation. This pathway involves phosphorylation of Tyr-454 and probably a putative host adaptor. Acts also via direct binding to the host cytoskeletal protein alpha-actinin in a NCK- and phosphotyrosine-independent manner. This interaction may stabilize the pedestal, but is not essential for its formation.<ref>PMID:10096089</ref> <ref>PMID:14757753</ref> <ref>PMID:14764108</ref> <ref>PMID:15813734</ref> <ref>PMID:17521329</ref> <ref>PMID:9390560</ref>	+	[[https://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref> [[https://www.uniprot.org/uniprot/TIR_ECO27 TIR_ECO27]] Multifunctional protein that is required for efficient pedestal formation in host epithelial cells during infection. The extracellular region acts as a receptor for bacterial intimin, allowing the bacterium to attach tightly to the host-cell surface. Simultaneously, the intracellular region initiates a signaling cascade in the host cell, which leads to actin polymerization and formation of actin pedestals at the sites of bacterial adhesion. In strain E2348/69, acts mainly via the host adaptor proteins NCK1 and NCK2. Once clustered and phosphorylated at Tyr-474, Tir binds to NCK proteins, which in turn bind and activate host WASL/N-WASP, leading to actin polymerization. Can also trigger an inefficient, NCK-independent pedestal formation. This pathway involves phosphorylation of Tyr-454 and probably a putative host adaptor. Acts also via direct binding to the host cytoskeletal protein alpha-actinin in a NCK- and phosphotyrosine-independent manner. This interaction may stabilize the pedestal, but is not essential for its formation.<ref>PMID:10096089</ref> <ref>PMID:14757753</ref> <ref>PMID:14764108</ref> <ref>PMID:15813734</ref> <ref>PMID:17521329</ref> <ref>PMID:9390560</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:44, 21 May 2019

OCA — Tue, 21 May 2019 07:44:05 GMT

←Older revision		Revision as of 07:44, 21 May 2019
Line 1:		Line 1:

	==Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir==		==Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir==
-	<StructureSection load='2ci9' size='340' side='right' caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='2ci9' size='340' side='right'caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Findeis, A C]]		[[Category: Findeis, A C]]
	[[Category: Frese, S]]		[[Category: Frese, S]]

OCA at 08:23, 23 May 2018

OCA — Wed, 23 May 2018 08:23:15 GMT

←Older revision		Revision as of 08:23, 23 May 2018
Line 1:		Line 1:
-	==~~NCK1~~ SH2-~~DOMAIN IN COMPLEX WITH A DODECAPHOSPHOPEPTIDE FROM~~ EPEC ~~PROTEIN TIR~~==	+
		+	==Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir==
	<StructureSection load='2ci9' size='340' side='right' caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2ci9' size='340' side='right' caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [http://pdbe.org/2ci9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ci9 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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [http://pdbe.org/2ci9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ci9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ci9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/2ci9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/2ci9_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=2ci9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 40:		Line 41:
	[[Category: Schubert, W D]]		[[Category: Schubert, W D]]
	[[Category: Stradal, T E.B]]		[[Category: Stradal, T E.B]]
		+	[[Category: Protein binding]]
	[[Category: Protein-binding]]		[[Category: Protein-binding]]
	[[Category: Sh2-domain-complex]]		[[Category: Sh2-domain-complex]]

OCA at 08:33, 11 September 2015

OCA — Fri, 11 Sep 2015 08:33:12 GMT

←Older revision		Revision as of 08:33, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2ci9' size='340' side='right' caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2ci9' size='340' side='right' caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ci9 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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [http://pdbe.org/2ci9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ci9 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref>	+	[[http://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref> [[http://www.uniprot.org/uniprot/TIR_ECO27 TIR_ECO27]] Multifunctional protein that is required for efficient pedestal formation in host epithelial cells during infection. The extracellular region acts as a receptor for bacterial intimin, allowing the bacterium to attach tightly to the host-cell surface. Simultaneously, the intracellular region initiates a signaling cascade in the host cell, which leads to actin polymerization and formation of actin pedestals at the sites of bacterial adhesion. In strain E2348/69, acts mainly via the host adaptor proteins NCK1 and NCK2. Once clustered and phosphorylated at Tyr-474, Tir binds to NCK proteins, which in turn bind and activate host WASL/N-WASP, leading to actin polymerization. Can also trigger an inefficient, NCK-independent pedestal formation. This pathway involves phosphorylation of Tyr-454 and probably a putative host adaptor. Acts also via direct binding to the host cytoskeletal protein alpha-actinin in a NCK- and phosphotyrosine-independent manner. This interaction may stabilize the pedestal, but is not essential for its formation.<ref>PMID:10096089</ref> <ref>PMID:14757753</ref> <ref>PMID:14764108</ref> <ref>PMID:15813734</ref> <ref>PMID:17521329</ref> <ref>PMID:9390560</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 2ci9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Findeis, A C]]		[[Category: Findeis, A C]]
	[[Category: Frese, S]]		[[Category: Frese, S]]

OCA at 13:55, 25 December 2014

OCA — Thu, 25 Dec 2014 13:55:20 GMT

←Older revision		Revision as of 13:55, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ci9 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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ci9 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Findeis, A C.]]	+	[[Category: Findeis, A C]]
-	[[Category: Frese, S.]]	+	[[Category: Frese, S]]
-	[[Category: Heinz, D W.]]	+	[[Category: Heinz, D W]]
-	[[Category: Marquardt, T.]]	+	[[Category: Marquardt, T]]
-	[[Category: Roske, Y S.]]	+	[[Category: Roske, Y S]]
-	[[Category: Schubert, W D.]]	+	[[Category: Schubert, W D]]
-	[[Category: Stradal, T E.B.]]	+	[[Category: Stradal, T E.B]]
	[[Category: Protein-binding]]		[[Category: Protein-binding]]
	[[Category: Sh2-domain-complex]]		[[Category: Sh2-domain-complex]]

OCA at 10:49, 3 October 2014

OCA — Fri, 03 Oct 2014 10:49:21 GMT

←Older revision		Revision as of 10:49, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2ci9\| PDB=2ci9 \| SCENE= }}~~	+	==NCK1 SH2-DOMAIN IN COMPLEX WITH A DODECAPHOSPHOPEPTIDE FROM EPEC PROTEIN TIR==
-	===NCK1 SH2-DOMAIN IN COMPLEX WITH A DODECAPHOSPHOPEPTIDE FROM EPEC PROTEIN TIR===	+	<StructureSection load='2ci9' size='340' side='right' caption='[[2ci9]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_16636066}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ci9]] is a 4 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=2CI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CI9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ci8\|2ci8]], [[2cia\|2cia]], [[2cub\|2cub]]</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=2ci9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ci9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ci9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ci9 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/ci/2ci9_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 ==
		+	Nck proteins are essential Src homology (SH) 2 and SH3 domain-bearing adapters that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. Two mammalian pathogens, enteropathogenic Escherichia coli and vaccinia virus, exploit Nck as part of their infection strategy. Conflicting data indicate potential differences in the recognition specificities of the SH2 domains of the isoproteins Nck1 (Nckalpha) and Nck2 (Nckbeta and Grb4). We have characterized the binding specificities of both SH2 domains and find them to be essentially indistinguishable. Crystal structures of both domains in complex with phosphopeptides derived from the enteropathogenic E. coli protein Tir concur in identifying highly conserved, specific recognition of the phosphopeptide. Differential peptide recognition can therefore not account for the preference of either Nck in particular signaling pathways. Binding studies using sequentially mutated, high affinity phosphopeptides establish the sequence variability tolerated in peptide recognition. Based on this binding motif, we identify potential new binding partners of Nck1 and Nck2 and confirm this experimentally for the Arf-GAP GIT1.

-	~~==Function==~~	+	The phosphotyrosine peptide binding specificity of Nck1 and Nck2 Src homology 2 domains.,Frese S, Schubert WD, Findeis AC, Marquardt T, Roske YS, Stradal TE, Heinz DW J Biol Chem. 2006 Jun 30;281(26):18236-45. Epub 2006 Apr 24. PMID:16636066<ref>PMID:16636066</ref>
-	~~[[http://www~~.~~uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors~~, ~~such as KDR and PDGFRB~~, ~~or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response~~, ~~not in the detection of the damage by ATM/ATR~~, ~~but for efficient activation of downstream effectors~~, ~~such as that of CHEK2~~. ~~Plays a role in ELK1~~-~~dependent transcriptional activation in response to activated Ras signaling~~.~~<ref>~~PMID:~~10026169</ref> <ref>PMID:16835242</ref>~~ <ref>PMID:~~17803907~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2ci9]] is~~ a ~~4 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=2CI9 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:016636066</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Findeis, A C.]]		[[Category: Findeis, A C.]]

OCA at 08:54, 23 April 2014

OCA — Wed, 23 Apr 2014 08:54:02 GMT

←Older revision		Revision as of 08:54, 23 April 2014
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-	[[Image:2ci9.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ci9", 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_2ci9\| PDB=2ci9 \| SCENE= }}		{{STRUCTURE_2ci9\| PDB=2ci9 \| SCENE= }}
-
	===NCK1 SH2-DOMAIN IN COMPLEX WITH A DODECAPHOSPHOPEPTIDE FROM EPEC PROTEIN TIR===		===NCK1 SH2-DOMAIN IN COMPLEX WITH A DODECAPHOSPHOPEPTIDE FROM EPEC PROTEIN TIR===
		+	{{ABSTRACT_PUBMED_16636066}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/NCK1_HUMAN NCK1_HUMAN]] Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling.<ref>PMID:10026169</ref> <ref>PMID:16835242</ref> <ref>PMID:17803907</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_16636066}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov)~~, ~~where 16636066 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_16636066}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:016636066</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016636066</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Findeis, A C.]]		[[Category: Findeis, A C.]]

OCA: Protected "2ci9" [edit=sysop:move=sysop]

OCA — Wed, 24 Aug 2011 05:56:24 GMT

Protected "2ci9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:56, 24 August 2011

OCA at 05:56, 24 August 2011

OCA — Wed, 24 Aug 2011 05:56:22 GMT

←Older revision		Revision as of 05:56, 24 August 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ci9.png\|left\|200px]]		[[Image:2ci9.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2CI9~~ is a 4 ~~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=2CI9 OCA].	+	[[2ci9]] is a 4 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=2CI9 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16636066~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016636066</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Findeis, A C.]]		[[Category: Findeis, A C.]]
Line 32:		Line 31:
	[[Category: Schubert, W D.]]		[[Category: Schubert, W D.]]
	[[Category: Stradal, T E.B.]]		[[Category: Stradal, T E.B.]]
-	[[Category: ~~Binding specificity]]~~	+	[[Category: Protein-binding]]
-	~~[[Category: Host~~-~~pathogen]]~~	+	[[Category: Sh2-domain-complex]]
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Repeat~~]]	+
-	[[Category: Sh2-domain]]	+
-	~~[[Category: Sh3 domain]]~~	+
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:00:01 2009''~~	+