7nyl - Revision history

OCA at 12:41, 1 February 2024

2024-02-01T12:41:47Z

← Older revision		Revision as of 12:41, 1 February 2024
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	<StructureSection load='7nyl' size='340' side='right'caption='[[7nyl]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='7nyl' size='340' side='right'caption='[[7nyl]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7nyl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NYL FirstGlance]. <br>		<table><tr><td colspan='2'>[[7nyl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NYL FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GLC:ALPHA-D~~-~~GLUCOSE'>GLC</scene>~~, ~~<scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.95Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[7nyk\|7nyk]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PRD_900006:trehalose'>PRD_900006</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Phosphoinositide_5-phosphatase Phosphoinositide 5-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.36 3.1.3.36]~~ </~~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=7nyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nyl OCA], [https://pdbe.org/7nyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nyl RCSB], [https://www.ebi.ac.uk/pdbsum/7nyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nyl 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=7nyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nyl OCA], [https://pdbe.org/7nyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nyl RCSB], [https://www.ebi.ac.uk/pdbsum/7nyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nyl ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[https://www.uniprot.org/uniprot/JIP1_HUMAN JIP1_HUMAN]] Defects in MAPK8IP1 are a cause of non-insulin-dependent diabetes mellitus (NIDDM) [MIM:[https://omim.org/entry/125853 125853]]. NIDDM is characterized by an autosomal dominant mode of inheritance, onset during adulthood and insulin resistance.<ref>PMID:10700186</ref>		[https://www.uniprot.org/uniprot/JIP1_HUMAN JIP1_HUMAN] Defects in MAPK8IP1 are a cause of non-insulin-dependent diabetes mellitus (NIDDM) [MIM:[https://omim.org/entry/125853 125853]. NIDDM is characterized by an autosomal dominant mode of inheritance, onset during adulthood and insulin resistance.<ref>PMID:10700186</ref>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/JIP1_HUMAN JIP1_HUMAN]] The JNK-interacting protein (JIP) group of scaffold proteins selectively mediates JNK signaling by aggregating specific components of the MAPK cascade to form a functional JNK signaling module. Required for JNK activation in response to excitotoxic stress. Cytoplasmic MAPK8IP1 causes inhibition of JNK-regulated activity by retaining JNK in the cytoplasm and inhibiting JNK phosphorylation of c-Jun. May also participate in ApoER2-specific reelin signaling. Directly, or indirectly, regulates GLUT2 gene expression and beta-cell function. Appears to have a role in cell signaling in mature and developing nerve terminals. May function as a regulator of vesicle transport, through interactions with the JNK-signaling components and motor proteins (By similarity). Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response.		[https://www.uniprot.org/uniprot/JIP1_HUMAN JIP1_HUMAN] The JNK-interacting protein (JIP) group of scaffold proteins selectively mediates JNK signaling by aggregating specific components of the MAPK cascade to form a functional JNK signaling module. Required for JNK activation in response to excitotoxic stress. Cytoplasmic MAPK8IP1 causes inhibition of JNK-regulated activity by retaining JNK in the cytoplasm and inhibiting JNK phosphorylation of c-Jun. May also participate in ApoER2-specific reelin signaling. Directly, or indirectly, regulates GLUT2 gene expression and beta-cell function. Appears to have a role in cell signaling in mature and developing nerve terminals. May function as a regulator of vesicle transport, through interactions with the JNK-signaling components and motor proteins (By similarity). Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Phosphoinositide 5-phosphatase]]~~		[[Category: Ielasi FS]]
	[[Category: Ielasi~~, F S~~]]		[[Category: Jensen MR]]
	[[Category: Jensen~~, M R~~]]		[[Category: Palencia A]]
	[[Category: Palencia, A]]		[[Category: Perez LM]]
	[[Category: Perez~~, L M]]~~
	~~[[Category: Signaling protein~~]]

OCA at 07:29, 2 March 2022

2022-03-02T07:29:17Z

← Older revision		Revision as of 07:29, 2 March 2022
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	==Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)==		==Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)==
	<StructureSection load='7nyl' size='340' side='right'caption='[[7nyl]]' scene=''>		<StructureSection load='7nyl' size='340' side='right'caption='[[7nyl]], [[Resolution\|resolution]] 1.95Å' 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=7NYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NYL FirstGlance]. <br>		<table><tr><td colspan='2'>[[7nyl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NYL 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=7nyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nyl OCA], [https://pdbe.org/7nyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nyl RCSB], [https://www.ebi.ac.uk/pdbsum/7nyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nyl 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7nyk\|7nyk]]</div></td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphoinositide_5-phosphatase Phosphoinositide 5-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.36 3.1.3.36] </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=7nyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nyl OCA], [https://pdbe.org/7nyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nyl RCSB], [https://www.ebi.ac.uk/pdbsum/7nyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nyl ProSAT]</span></td></tr>
	</table>		</table>
			== Disease ==
			[[https://www.uniprot.org/uniprot/JIP1_HUMAN JIP1_HUMAN]] Defects in MAPK8IP1 are a cause of non-insulin-dependent diabetes mellitus (NIDDM) [MIM:[https://omim.org/entry/125853 125853]]. NIDDM is characterized by an autosomal dominant mode of inheritance, onset during adulthood and insulin resistance.<ref>PMID:10700186</ref>
			== Function ==
			[[https://www.uniprot.org/uniprot/JIP1_HUMAN JIP1_HUMAN]] The JNK-interacting protein (JIP) group of scaffold proteins selectively mediates JNK signaling by aggregating specific components of the MAPK cascade to form a functional JNK signaling module. Required for JNK activation in response to excitotoxic stress. Cytoplasmic MAPK8IP1 causes inhibition of JNK-regulated activity by retaining JNK in the cytoplasm and inhibiting JNK phosphorylation of c-Jun. May also participate in ApoER2-specific reelin signaling. Directly, or indirectly, regulates GLUT2 gene expression and beta-cell function. Appears to have a role in cell signaling in mature and developing nerve terminals. May function as a regulator of vesicle transport, through interactions with the JNK-signaling components and motor proteins (By similarity). Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips-that is, 180 degrees rotations-despite their role in maintaining the protein fold(1-3). It was suggested that large-scale 'breathing' motions of the surrounding protein environment would be necessary to accommodate these ring flipping events(1). However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa.

			Visualizing protein breathing motions associated with aromatic ring flipping.,Marino Perez L, Ielasi FS, Bessa LM, Maurin D, Kragelj J, Blackledge M, Salvi N, Bouvignies G, Palencia A, Jensen MR Nature. 2022 Feb;602(7898):695-700. doi: 10.1038/s41586-022-04417-6. Epub 2022, Feb 16. PMID:35173330<ref>PMID:35173330</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7nyl" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ielasi FS]]		[[Category: Phosphoinositide 5-phosphatase]]
	[[Category: Jensen MR]]		[[Category: Ielasi, F S]]
	[[Category: Palencia A]]		[[Category: Jensen, M R]]
	[[Category: Perez LM]]		[[Category: Palencia, A]]
			[[Category: Perez, L M]]
			[[Category: Signaling protein]]

OCA at 15:26, 22 December 2021

2021-12-22T15:26:45Z

← Older revision		Revision as of 15:26, 22 December 2021
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7nyl is ~~ON HOLD until Paper Publication~~		==Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)==
			<StructureSection load='7nyl' size='340' side='right'caption='[[7nyl]]' scene=''>
	~~Authors~~: ~~Perez~~, L.M., ~~Ielasi~~, F.S., ~~Palencia, A~~., ~~Jensen, M~~.R.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NYL FirstGlance]. <br>
	~~Description: Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)~~		</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=7nyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nyl OCA], [https://pdbe.org/7nyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nyl RCSB], [https://www.ebi.ac.uk/pdbsum/7nyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nyl ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Perez, L.M~~]]		__TOC__
	[[Category: ~~Ielasi, F.S~~]]		</StructureSection>
	[[Category: Palencia, A]]		[[Category: Large Structures]]
	[[Category: ~~Jensen, M.R~~]]		[[Category: Ielasi FS]]
			[[Category: Jensen MR]]
			[[Category: Palencia A]]
			[[Category: Perez LM]]

OCA at 13:43, 17 June 2021

2021-06-17T13:43:23Z

← Older revision		Revision as of 13:43, 17 June 2021
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	Authors: Perez, L.M., Ielasi, F.S., Palencia, A., Jensen, M.R.		Authors: Perez, L.M., Ielasi, F.S., Palencia, A., Jensen, M.R.

	Description: SH3 domain of JNK-interacting Protein 1 (JIP1)		Description: Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	~~[[Category: Jensen, M.R]]~~
	[[Category: Perez, L.M]]		[[Category: Perez, L.M]]
	[[Category: Ielasi, F.S]]		[[Category: Ielasi, F.S]]
	[[Category: Palencia, A]]		[[Category: Palencia, A]]
			[[Category: Jensen, M.R]]

OCA at 06:32, 21 April 2021

2021-04-21T06:32:48Z

← Older revision		Revision as of 06:32, 21 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Perez, L.M., Ielasi, F.S., Palencia, A., Jensen, M.R.		Authors: Perez, L.M., Ielasi, F.S., Palencia, A., Jensen, M.R.

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

2021-03-31T09:33:11Z

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

← Older revision	Revision as of 09:33, 31 March 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7nyl is ON HOLD Authors: Perez, L.M., Ielasi, F.S., Palencia, A., Jensen, M.R. Description: SH3 domain of JNK-interacting Protein 1 (JIP1) [[Catego...

2021-03-31T09:33:10Z

New page: '''Unreleased structure''' The entry 7nyl is ON HOLD Authors: Perez, L.M., Ielasi, F.S., Palencia, A., Jensen, M.R. Description: SH3 domain of JNK-interacting Protein 1 (JIP1) [[Catego...

New page

'''Unreleased structure'''

The entry 7nyl is ON HOLD

Authors: Perez, L.M., Ielasi, F.S., Palencia, A., Jensen, M.R.

Description: SH3 domain of JNK-interacting Protein 1 (JIP1)
[[Category: Unreleased Structures]]
[[Category: Jensen, M.R]]
[[Category: Perez, L.M]]
[[Category: Ielasi, F.S]]
[[Category: Palencia, A]]