7ner - Revision history

OCA at 07:43, 11 February 2026

2026-02-11T07:43:08Z

← Older revision		Revision as of 07:43, 11 February 2026
Line 3:		Line 3:
	<StructureSection load='7ner' size='340' side='right'caption='[[7ner]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='7ner' size='340' side='right'caption='[[7ner]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7ner]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NER FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NER FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.55Å</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]] 1.55Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ner FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ner OCA], [https://pdbe.org/7ner PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ner RCSB], [https://www.ebi.ac.uk/pdbsum/7ner PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ner 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=7ner FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ner OCA], [https://pdbe.org/7ner PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ner RCSB], [https://www.ebi.ac.uk/pdbsum/7ner PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ner ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/SRC_CHICK SRC_CHICK] Non-receptor protein tyrosine kinase which is activated following engagement of many different classes of cellular receptors including immune response receptors, integrins and other adhesion receptors, receptor protein tyrosine kinases, G protein-coupled receptors as well as cytokine receptors. Participates in signaling pathways that control a diverse spectrum of biological activities including gene transcription, immune response, cell adhesion, cell cycle progression, apoptosis, migration, and transformation. Due to functional redundancy between members of the SRC kinase family, identification of the specific role of each SRC kinase is very difficult. SRC appears to be one of the primary kinases activated following engagement of receptors and plays a role in the activation of other protein tyrosine kinase (PTK) families. Receptor clustering or dimerization leads to recruitment of SRC to the receptor complexes where it phosphorylates the tyrosine residues within the receptor cytoplasmic domains. Plays an important role in the regulation of cytoskeletal organization through phosphorylation of specific substrates involved in this process. When cells adhere via focal adhesions to the extra-cellular matrix, signals are transmitted by integrins into the cell and result in tyrosine phosphorylation of a number of focal adhesion proteins, including PTK2/FAK1 and paxillin (PXN). Also active at the sites of cell-cell contact adherens junctions and at gap junctions. Implicated in the regulation of pre-mRNA-processing. Might be involved not only in mediating the transduction of mitogenic signals at the level of the plasma membrane but also in controlling progression through the cell cycle via interaction with regulatory proteins in the nucleus.<ref>PMID:1717492</ref> <ref>PMID:8550628</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Src kinase belongs to the family of Src-related nonreceptor tyrosine kinases. Because of its physiological role in cell growth and proliferation, its activity is strictly controlled by several mechanisms. Nevertheless, in viral Src kinase (v-Src) some of these mechanisms fail, and its uncontrolled activity is responsible for the occurrence of cancer. Here, the crystal structures of three SH3-domain mutants of v-Src were determined to unveil the effects of these oncogenic mutations in this regulatory domain. Mutations in the n-Src and distal loops have a low impact on the overall structure of the domain and its capacity to form intertwined dimers. However, mutations in the RT loop compromise the stability of the domain and make the protein very prone to aggregation. Additionally, these mutations prevent the formation of intertwined dimers. The results show a synergistic effect between mutations in the RT loop and those in the n-Src and distal loops. Analysis of the structures of the v-Src SH3-domain mutants and the closed inactive conformation of cellular Src kinase (c-Src) point to a loss of the interactions that are required to establish the compact inactive form of the kinase. Nevertheless, an analysis of structures of the c-Src SH3 domain complexed with class I and II peptides points to minor changes in the interactions between the v-Src SH3 domain and these peptides. In this way, the structures reported here indicate that mutations in the RT loop might impair the kinase regulation mechanism without affecting the recognition of short proline-rich motifs in the target proteins of the kinase, thus explaining the oncogenic behaviour of the protein.

	The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain.,Salinas-Garcia MC, Plaza-Garrido M, Camara-Artigas A Acta Crystallogr D Struct Biol. 2021 Jun 1;77(Pt 6):854-866. doi:, 10.1107/S2059798321004344. Epub 2021 May 19. PMID:34076598<ref>PMID:34076598</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7ner" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Tyrosine kinase 3D structures\|Tyrosine kinase 3D structures]]		*[[Tyrosine kinase 3D structures\|Tyrosine kinase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Gallus gallus]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Camara-Artigas A]]		[[Category: Camara-Artigas A]]
	[[Category: Salinas-Garcia MC]]		[[Category: Salinas-Garcia MC]]

OCA at 12:34, 1 February 2024

2024-02-01T12:34:01Z

← Older revision		Revision as of 12:34, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7ner' size='340' side='right'caption='[[7ner]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='7ner' size='340' side='right'caption='[[7ner]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ner]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Chick Chick~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NER FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ner]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NER FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.55Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ner FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ner OCA], [https://pdbe.org/7ner PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ner RCSB], [https://www.ebi.ac.uk/pdbsum/7ner PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ner 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=7ner FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ner OCA], [https://pdbe.org/7ner PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ner RCSB], [https://www.ebi.ac.uk/pdbsum/7ner PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ner ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/SRC_CHICK SRC_CHICK] Non-receptor protein tyrosine kinase which is activated following engagement of many different classes of cellular receptors including immune response receptors, integrins and other adhesion receptors, receptor protein tyrosine kinases, G protein-coupled receptors as well as cytokine receptors. Participates in signaling pathways that control a diverse spectrum of biological activities including gene transcription, immune response, cell adhesion, cell cycle progression, apoptosis, migration, and transformation. Due to functional redundancy between members of the SRC kinase family, identification of the specific role of each SRC kinase is very difficult. SRC appears to be one of the primary kinases activated following engagement of receptors and plays a role in the activation of other protein tyrosine kinase (PTK) families. Receptor clustering or dimerization leads to recruitment of SRC to the receptor complexes where it phosphorylates the tyrosine residues within the receptor cytoplasmic domains. Plays an important role in the regulation of cytoskeletal organization through phosphorylation of specific substrates involved in this process. When cells adhere via focal adhesions to the extra-cellular matrix, signals are transmitted by integrins into the cell and result in tyrosine phosphorylation of a number of focal adhesion proteins, including PTK2/FAK1 and paxillin (PXN). Also active at the sites of cell-cell contact adherens junctions and at gap junctions. Implicated in the regulation of pre-mRNA-processing. Might be involved not only in mediating the transduction of mitogenic signals at the level of the plasma membrane but also in controlling progression through the cell cycle via interaction with regulatory proteins in the nucleus.<ref>PMID:1717492</ref> <ref>PMID:8550628</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7ner" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ner" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Tyrosine kinase 3D structures\|Tyrosine kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Chick~~]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Camara-Artigas, A]]		[[Category: Camara-Artigas A]]
	[[Category: Salinas-Garcia~~, M C]]~~		[[Category: Salinas-Garcia MC]]
	~~[[Category: Beta barrel]]~~
	~~[[Category: Protein binding]]~~
	~~[[Category: Sh3 domain~~]]

OCA at 15:02, 17 June 2021

2021-06-17T15:02:01Z

← Older revision		Revision as of 15:02, 17 June 2021
Line 1:		Line 1:

	==Crystal structure of the v-Src SH3 domain Q128R mutant==		==Crystal structure of the v-Src SH3 domain Q128R mutant==
	<StructureSection load='7ner' size='340' side='right'caption='[[7ner]]' scene=''>		<StructureSection load='7ner' size='340' side='right'caption='[[7ner]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NER FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ner]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NER FirstGlance]. <br>
	</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=7ner FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ner OCA], [https://pdbe.org/7ner PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ner RCSB], [https://www.ebi.ac.uk/pdbsum/7ner PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ner ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ner FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ner OCA], [https://pdbe.org/7ner PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ner RCSB], [https://www.ebi.ac.uk/pdbsum/7ner PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ner ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Src kinase belongs to the family of Src-related nonreceptor tyrosine kinases. Because of its physiological role in cell growth and proliferation, its activity is strictly controlled by several mechanisms. Nevertheless, in viral Src kinase (v-Src) some of these mechanisms fail, and its uncontrolled activity is responsible for the occurrence of cancer. Here, the crystal structures of three SH3-domain mutants of v-Src were determined to unveil the effects of these oncogenic mutations in this regulatory domain. Mutations in the n-Src and distal loops have a low impact on the overall structure of the domain and its capacity to form intertwined dimers. However, mutations in the RT loop compromise the stability of the domain and make the protein very prone to aggregation. Additionally, these mutations prevent the formation of intertwined dimers. The results show a synergistic effect between mutations in the RT loop and those in the n-Src and distal loops. Analysis of the structures of the v-Src SH3-domain mutants and the closed inactive conformation of cellular Src kinase (c-Src) point to a loss of the interactions that are required to establish the compact inactive form of the kinase. Nevertheless, an analysis of structures of the c-Src SH3 domain complexed with class I and II peptides points to minor changes in the interactions between the v-Src SH3 domain and these peptides. In this way, the structures reported here indicate that mutations in the RT loop might impair the kinase regulation mechanism without affecting the recognition of short proline-rich motifs in the target proteins of the kinase, thus explaining the oncogenic behaviour of the protein.

			The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain.,Salinas-Garcia MC, Plaza-Garrido M, Camara-Artigas A Acta Crystallogr D Struct Biol. 2021 Jun 1;77(Pt 6):854-866. doi:, 10.1107/S2059798321004344. Epub 2021 May 19. PMID:34076598<ref>PMID:34076598</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7ner" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Chick]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Camara-Artigas A]]		[[Category: Camara-Artigas, A]]
	[[Category: Salinas-Garcia MC]]		[[Category: Salinas-Garcia, M C]]
			[[Category: Beta barrel]]
			[[Category: Protein binding]]
			[[Category: Sh3 domain]]

OCA at 14:36, 2 June 2021

2021-06-02T14:36:35Z

← Older revision		Revision as of 14:36, 2 June 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7ner is ~~ON HOLD until Paper Publication~~		==Crystal structure of the v-Src SH3 domain Q128R mutant==
			<StructureSection load='7ner' size='340' side='right'caption='[[7ner]]' scene=''>
	~~Authors~~: ~~Camara~~-~~Artigas~~, A., ~~Salinas-Garcia~~, M.C.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NER FirstGlance]. <br>
	~~Description: Crystal structure of the v-Src SH3 domain Q128R mutant~~		</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=7ner FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ner OCA], [https://pdbe.org/7ner PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ner RCSB], [https://www.ebi.ac.uk/pdbsum/7ner PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ner ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: Camara-Artigas, A]]		__TOC__
	[[Category: Salinas-Garcia~~, M.C~~]]		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Camara-Artigas A]]
			[[Category: Salinas-Garcia MC]]

OCA at 05:29, 17 March 2021

2021-03-17T05:29:30Z

← Older revision		Revision as of 05:29, 17 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7ner is ON HOLD		The entry 7ner is ON HOLD until Paper Publication

	Authors: Camara-Artigas, A., Salinas-Garcia, M.C.		Authors: Camara-Artigas, A., Salinas-Garcia, M.C.
Line 7:		Line 7:
	Description: Crystal structure of the v-Src SH3 domain Q128R mutant		Description: Crystal structure of the v-Src SH3 domain Q128R mutant
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Camara-Artigas, A]]
	[[Category: Salinas-Garcia, M.C]]		[[Category: Salinas-Garcia, M.C]]
	~~[[Category: Camara-Artigas, A]]~~

OCA: Protected "7ner" [edit=sysop:move=sysop]

2021-02-10T09:27:49Z

Protected "7ner" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:27, 10 February 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7ner is ON HOLD Authors: Camara-Artigas, A., Salinas-Garcia, M.C. Description: Crystal structure of the v-Src SH3 domain Q128R mutant [[Category: U...

2021-02-10T09:27:48Z

New page: '''Unreleased structure''' The entry 7ner is ON HOLD Authors: Camara-Artigas, A., Salinas-Garcia, M.C. Description: Crystal structure of the v-Src SH3 domain Q128R mutant [[Category: U...

New page

'''Unreleased structure'''

The entry 7ner is ON HOLD

Authors: Camara-Artigas, A., Salinas-Garcia, M.C.

Description: Crystal structure of the v-Src SH3 domain Q128R mutant
[[Category: Unreleased Structures]]
[[Category: Salinas-Garcia, M.C]]
[[Category: Camara-Artigas, A]]