5qu6 - Revision history

OCA at 11:28, 21 February 2024

OCA — Wed, 21 Feb 2024 11:28:08 GMT

←Older revision		Revision as of 11:28, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='5qu6' size='340' side='right'caption='[[5qu6]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='5qu6' size='340' side='right'caption='[[5qu6]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5qu6]] is a 28 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=5QU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QU6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5qu6]] is a 28 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=5QU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QU6 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~NCK1~~, ~~NCK (~~[~~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]] 1.816Å</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=5qu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qu6 OCA], [https://pdbe.org/5qu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qu6 RCSB], [https://www.ebi.ac.uk/pdbsum/5qu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qu6 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=5qu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qu6 OCA], [https://pdbe.org/5qu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qu6 RCSB], [https://www.ebi.ac.uk/pdbsum/5qu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qu6 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/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>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3 subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3 that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3.1). Inhibition of this protein/protein interaction ameliorated inflammatory symptoms in mouse models of multiple sclerosis, psoriasis, and asthma. A small molecule, AX-024, was reported to inhibit the Nck/CD3 interaction by physically binding to the Nck1-SH3.1 domain, suggesting a route to develop an inhibitor of the Nck1/CD3 interaction for modulating TCR activity in autoimmune and inflammatory diseases. We show here that AX-024 reduces T cell proliferation upon weak TCR stimulation but does not significantly affect phosphorylation of Zap70 (zeta chain of T cell receptor-associated protein kinase 70). We also find that AX-024 is likely not involved in modulating the Nck/TCR interaction but probably has other targets in T cells. An array of biophysical techniques did not detect a direct interaction between AX-024 and Nck-SH3.1 in vitro Crystal structures of the Nck-SH3.1 domain revealed its binding mode to the PRS in CD3. The SH3 domain tends to generate homodimers through a domain swap. Domain swaps observed previously in other SH3 domains indicate a general propensity of this protein fold to exchange structural elements. The swapped form of Nck-SH3.1 is unable to bind CD3, possibly representing an inactive form of Nck in cells.	+
-		+
-	Small molecule AX-024 reduces T cell proliferation independently of CD3/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain.,Richter K, Rufer AC, Muller M, Burger D, Casagrande F, Grossenbacher T, Huber S, Hug MN, Koldewey P, D'Osualdo A, Schlatter D, Stoll T, Rudolph MG J Biol Chem. 2020 Jun 5;295(23):7849-7864. doi: 10.1074/jbc.RA120.012788. Epub, 2020 Apr 21. PMID:32317279<ref>PMID:32317279</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5qu6" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rudolph~~, M G]]~~	+	[[Category: Rudolph MG]]
-	~~[[Category: Adaptor]]~~	+
-	~~[[Category: Domain swap]]~~	+
-	~~[[Category: Peptide binding]]~~	+
-	~~[[Category: Sh3 domain]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 03:39, 2 July 2021

OCA — Fri, 02 Jul 2021 03:39:35 GMT

←Older revision		Revision as of 03:39, 2 July 2021
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	== 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/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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3 subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3 that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3.1). Inhibition of this protein/protein interaction ameliorated inflammatory symptoms in mouse models of multiple sclerosis, psoriasis, and asthma. A small molecule, AX-024, was reported to inhibit the Nck/CD3 interaction by physically binding to the Nck1-SH3.1 domain, suggesting a route to develop an inhibitor of the Nck1/CD3 interaction for modulating TCR activity in autoimmune and inflammatory diseases. We show here that AX-024 reduces T cell proliferation upon weak TCR stimulation but does not significantly affect phosphorylation of Zap70 (zeta chain of T cell receptor-associated protein kinase 70). We also find that AX-024 is likely not involved in modulating the Nck/TCR interaction but probably has other targets in T cells. An array of biophysical techniques did not detect a direct interaction between AX-024 and Nck-SH3.1 in vitro Crystal structures of the Nck-SH3.1 domain revealed its binding mode to the PRS in CD3. The SH3 domain tends to generate homodimers through a domain swap. Domain swaps observed previously in other SH3 domains indicate a general propensity of this protein fold to exchange structural elements. The swapped form of Nck-SH3.1 is unable to bind CD3, possibly representing an inactive form of Nck in cells.
		+
		+	Small molecule AX-024 reduces T cell proliferation independently of CD3/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain.,Richter K, Rufer AC, Muller M, Burger D, Casagrande F, Grossenbacher T, Huber S, Hug MN, Koldewey P, D'Osualdo A, Schlatter D, Stoll T, Rudolph MG J Biol Chem. 2020 Jun 5;295(23):7849-7864. doi: 10.1074/jbc.RA120.012788. Epub, 2020 Apr 21. PMID:32317279<ref>PMID:32317279</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5qu6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:28, 12 May 2021

OCA — Wed, 12 May 2021 09:28:29 GMT

←Older revision		Revision as of 09:28, 12 May 2021
Line 3:		Line 3:
	<StructureSection load='5qu6' size='340' side='right'caption='[[5qu6]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='5qu6' size='340' side='right'caption='[[5qu6]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5qu6]] is a 28 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QU6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5QU6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5qu6]] is a 28 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=5QU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QU6 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5qu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qu6 OCA], [~~http~~://pdbe.org/5qu6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5qu6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5qu6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5qu6 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NCK1, NCK ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5qu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qu6 OCA], [https://pdbe.org/5qu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qu6 RCSB], [https://www.ebi.ac.uk/pdbsum/5qu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qu6 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>	+	[[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>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Rudolph, M G]]		[[Category: Rudolph, M G]]

OCA at 04:06, 13 February 2020

OCA — Thu, 13 Feb 2020 04:06:37 GMT

←Older revision		Revision as of 04:06, 13 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5qu6 is ON HOLD~~	+	==Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic==
-		+	<StructureSection load='5qu6' size='340' side='right'caption='[[5qu6]], [[Resolution\|resolution]] 1.82Å' scene=''>
-	~~Authors: Rudolph, M.G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5qu6]] is a 28 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QU6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5QU6 FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic	+	</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=5qu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qu6 OCA], [http://pdbe.org/5qu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qu6 RCSB], [http://www.ebi.ac.uk/pdbsum/5qu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qu6 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Rudolph, M.G]]	+	== 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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rudolph, M G]]
		+	[[Category: Adaptor]]
		+	[[Category: Domain swap]]
		+	[[Category: Peptide binding]]
		+	[[Category: Sh3 domain]]
		+	[[Category: Signaling protein]]

OCA at 06:00, 5 February 2020

OCA — Wed, 05 Feb 2020 06:00:17 GMT

←Older revision		Revision as of 06:00, 5 February 2020
Line 3:		Line 3:
	The entry 5qu6 is ON HOLD		The entry 5qu6 is ON HOLD

-	Authors: ~~Burger, D., Ruf, A., Benz, J., Schlatter, D.,~~ Rudolph, M.G.	+	Authors: Rudolph, M.G.

	Description: Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic		Description: Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Ruf, A]]
-	[[Category: Schlatter, D]]
-	[[Category: Burger, D]]
-	[[Category: Benz, J]]
	[[Category: Rudolph, M.G]]		[[Category: Rudolph, M.G]]

OCA at 07:01, 25 December 2019

OCA — Wed, 25 Dec 2019 07:01:37 GMT

←Older revision		Revision as of 07:01, 25 December 2019
Line 5:		Line 5:
	Authors: Burger, D., Ruf, A., Benz, J., Schlatter, D., Rudolph, M.G.		Authors: Burger, D., Ruf, A., Benz, J., Schlatter, D., Rudolph, M.G.

-	Description: ~~HUMAN ADAPTOR PROTEIN NCK FIRST~~ SH3 ~~DOMAIN~~, 1.~~816A, P1, Rfree=26.3%, 371-5~~, ~~SLS180409~~	+	Description: Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ruf, A]]		[[Category: Ruf, A]]

OCA: Protected "5qu6" [edit=sysop:move=sysop]

OCA — Wed, 18 Dec 2019 05:31:38 GMT

Protected "5qu6" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:31, 18 December 2019

OCA: New page: '''Unreleased structure''' The entry 5qu6 is ON HOLD Authors: Burger, D., Ruf, A., Benz, J., Schlatter, D., Rudolph, M.G. Description: HUMAN ADAPTOR PROTEIN NCK FIRST SH3 DOMAIN, 1.816...

OCA — Wed, 18 Dec 2019 05:31:36 GMT

New page: '''Unreleased structure''' The entry 5qu6 is ON HOLD Authors: Burger, D., Ruf, A., Benz, J., Schlatter, D., Rudolph, M.G. Description: HUMAN ADAPTOR PROTEIN NCK FIRST SH3 DOMAIN, 1.816...

New page

'''Unreleased structure'''

The entry 5qu6 is ON HOLD

Authors: Burger, D., Ruf, A., Benz, J., Schlatter, D., Rudolph, M.G.

Description: HUMAN ADAPTOR PROTEIN NCK FIRST SH3 DOMAIN, 1.816A, P1, Rfree=26.3%, 371-5, SLS180409
[[Category: Unreleased Structures]]
[[Category: Ruf, A]]
[[Category: Schlatter, D]]
[[Category: Burger, D]]
[[Category: Benz, J]]
[[Category: Rudolph, M.G]]