2fpd - Revision history

OCA at 09:07, 6 November 2024

2024-11-06T09:07:15Z

← Older revision		Revision as of 09:07, 6 November 2024
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	<StructureSection load='2fpd' size='340' side='right'caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2fpd' size='340' side='right'caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPD 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=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]] 2.05Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PRD_900006:trehalose'>PRD_900006</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;~~'>~~[[2fpe\|2fpe]], [[2fpf\|2fpf]]</div>~~</td><~~/tr>~~
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [https://pdbe.org/2fpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [https://www.ebi.ac.uk/pdbsum/2fpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpd 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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [https://pdbe.org/2fpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [https://www.ebi.ac.uk/pdbsum/2fpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/JIP1_RAT JIP1_RAT]] 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 thus inhibiting the 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. Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response (By similarity).		[https://www.uniprot.org/uniprot/JIP1_RAT JIP1_RAT] 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 thus inhibiting the 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. Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpd_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpd_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Buffalo rat]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Dar, I~~]]		[[Category: Rattus norvegicus]]
	[[Category: ~~Gajhede, M~~]]		[[Category: Dar I]]
	[[Category: ~~Kristensen, O~~]]		[[Category: Gajhede M]]
	[[Category: ~~All beta structure]]~~		[[Category: Kristensen O]]
	~~[[Category: Signaling protein~~]]

OCA at 15:31, 3 March 2021

2021-03-03T15:31:03Z

← Older revision		Revision as of 15:31, 3 March 2021
Line 1:		Line 1:

	==Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein==		==Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein==
	<StructureSection load='2fpd' size='340' side='right' caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2fpd' size='340' side='right'caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FPD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=~~TRE~~:~~TREHALOSE~~'>~~TRE~~</scene></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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fpe\|2fpe]], [[2fpf\|2fpf]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [~~http~~://pdbe.org/2fpd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fpd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpd 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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [https://pdbe.org/2fpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [https://www.ebi.ac.uk/pdbsum/2fpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/JIP1_RAT JIP1_RAT]] 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 thus inhibiting the 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. Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response (By similarity).		[[https://www.uniprot.org/uniprot/JIP1_RAT JIP1_RAT]] 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 thus inhibiting the 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. Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
			[[Category: Large Structures]]
	[[Category: Dar, I]]		[[Category: Dar, I]]
	[[Category: Gajhede, M]]		[[Category: Gajhede, M]]

OCA at 07:32, 23 May 2018

2018-05-23T07:32:30Z

← Older revision		Revision as of 07:32, 23 May 2018
Line 1:		Line 1:

	==Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein==		==Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein==
	<StructureSection load='2fpd' size='340' side='right' caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2fpd' size='340' side='right' caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [http://pdbe.org/2fpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [http://www.ebi.ac.uk/pdbsum/2fpd 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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [http://pdbe.org/2fpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [http://www.ebi.ac.uk/pdbsum/2fpd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpd_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpd_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=2fpd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:14, 11 September 2015

2015-09-11T13:14:08Z

← Older revision		Revision as of 13:14, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2fpd' size='340' side='right' caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2fpd' size='340' side='right' caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 ~~Rattus norvegicus~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [http://www.ebi.ac.uk/pdbsum/2fpd 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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [http://pdbe.org/2fpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [http://www.ebi.ac.uk/pdbsum/2fpd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2fpd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Rattus norvegicus~~]]		[[Category: Buffalo rat]]
	[[Category: Dar, I]]		[[Category: Dar, I]]
	[[Category: Gajhede, M]]		[[Category: Gajhede, M]]

OCA at 16:55, 25 December 2014

2014-12-25T16:55:17Z

← Older revision		Revision as of 16:55, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPD FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [http://www.ebi.ac.uk/pdbsum/2fpd 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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [http://www.ebi.ac.uk/pdbsum/2fpd PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/JIP1_RAT JIP1_RAT]] 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 thus inhibiting the 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. Functions as an anti-apoptotic protein and whose level seems to influence the beta-cell death or survival response (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Dar, I.]]		[[Category: Dar, I]]
	[[Category: Gajhede, M.]]		[[Category: Gajhede, M]]
	[[Category: Kristensen, O.]]		[[Category: Kristensen, O]]
	[[Category: All beta structure]]		[[Category: All beta structure]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

OCA at 10:47, 30 September 2014

2014-09-30T10:47:45Z

← Older revision		Revision as of 10:47, 30 September 2014
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	[[Image:~~2fpd~~.~~png~~\|~~left~~\|~~200px~~]]		==Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein==
			<StructureSection load='2fpd' size='340' side='right' caption='[[2fpd]], [[Resolution\|resolution]] 2.05Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2fpd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPD FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fpe\|2fpe]], [[2fpf\|2fpf]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mapk8ip1, Ib1, Jip1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=2fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpd RCSB], [http://www.ebi.ac.uk/pdbsum/2fpd 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/fp/2fpd_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 ==
			Islet-brain 1 (IB1 or JIP-1) is a scaffold protein that interacts with components of the c-Jun N-terminal kinase (JNK) signal-transduction pathway. IB1 is expressed at high levels in neurons and in pancreatic beta-cells, where it controls expression of several insulin-secretory components and secretion. IB1 has been shown to homodimerize, but neither the molecular mechanisms nor the function of dimerization have yet been characterized. Here, we show that IB1 homodimerizes through a novel and unique set of Src homology 3 (SH3)-SH3 interactions. X-ray crystallography studies show that the dimer interface covers a region usually engaged in PxxP-mediated ligand recognition, even though the IB1 SH3 domain lacks this motif. The highly stable IB1 homodimer can be significantly destabilized in vitro by three individual point mutations directed against key residues involved in dimerization. Each mutation reduces IB1-dependent basal JNK activity in 293T cells. Impaired dimerization also results in a reduction in glucose transporter type 2 expression and in glucose-dependent insulin secretion in pancreatic beta-cells. Taken together, these results indicate that IB1 homodimerization through its SH3 domain has pleiotropic effects including regulation of the insulin secretion process.

	~~{{STRUCTURE_2fpd\| PDB=2fpd \| SCENE= }}~~		A unique set of SH3-SH3 interactions controls IB1 homodimerization.,Kristensen O, Guenat S, Dar I, Allaman-Pillet N, Abderrahmani A, Ferdaoussi M, Roduit R, Maurer F, Beckmann JS, Kastrup JS, Gajhede M, Bonny C EMBO J. 2006 Feb 22;25(4):785-97. Epub 2006 Feb 2. PMID:16456539<ref>PMID:16456539</ref>

	~~===Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain~~ of the ~~ib1 scaffold protein===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16456539}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2fpd]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016456539<~~/~~ref~~><~~ref group="xtra">PMID:012756254</ref><references group="xtra"~~/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Dar, I.]]		[[Category: Dar, I.]]

OCA at 12:22, 23 January 2013

2013-01-23T12:22:47Z

← Older revision		Revision as of 12:22, 23 January 2013
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	[[Image:2fpd.png\|left\|200px]]		[[Image:2fpd.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2fpd", 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_2fpd\| PDB=2fpd \| SCENE= }}		{{STRUCTURE_2fpd\| PDB=2fpd \| SCENE= }}

	===Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein===		===Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16456539}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16456539 is the PubMed ID number.~~
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	{{ABSTRACT_PUBMED_16456539}}		{{ABSTRACT_PUBMED_16456539}}

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	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16456539~~</ref><ref group="xtra">PMID:~~9235893</ref><ref group="xtra">PMID:9442013</ref><ref group="xtra">PMID:12756254</ref><ref group="xtra">PMID:10490659~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016456539</ref><ref group="xtra">PMID:012756254</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Dar, I.]]		[[Category: Dar, I.]]

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

2011-03-15T00:15:11Z

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

← Older revision	Revision as of 00:15, 15 March 2011
(No difference)

OCA at 00:15, 15 March 2011

2011-03-15T00:15:10Z

← Older revision		Revision as of 00:15, 15 March 2011
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	~~{{Seed}}~~
	[[Image:2fpd.png\|left\|200px]]		[[Image:2fpd.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
	~~2FPD~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA].		[[2fpd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA].

	==Reference==		==Reference==
Line 29:		Line 28:
	[[Category: Kristensen, O.]]		[[Category: Kristensen, O.]]
	[[Category: All beta structure]]		[[Category: All beta structure]]
			[[Category: Signaling protein]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 22:24:45 2009''~~

OCA at 20:24, 17 February 2009

2009-02-17T20:24:48Z

← Older revision		Revision as of 20:24, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2FPD is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA].		2FPD is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPD OCA].

	==Reference==		==Reference==
	A unique set of SH3-SH3 interactions controls IB1 homodimerization., Kristensen O, Guenat S, Dar I, Allaman-Pillet N, Abderrahmani A, Ferdaoussi M, Roduit R, Maurer F, Beckmann JS, Kastrup JS, Gajhede M, Bonny C, EMBO J. 2006 Feb 22;25(4):785-97. Epub 2006 Feb 2. PMID:~~[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/16456539 16456539]~~		<ref group="xtra">PMID:16456539</ref><ref group="xtra">PMID:9235893</ref><ref group="xtra">PMID:9442013</ref><ref group="xtra">PMID:12756254</ref><ref group="xtra">PMID:10490659</ref><references group="xtra"/>

	A cytoplasmic inhibitor of the JNK signal transduction pathway., Dickens M, Rogers JS, Cavanagh J, Raitano A, Xia Z, Halpern JR, Greenberg ME, Sawyers CL, Davis RJ, Science. 1997 Aug 1;277(5326):693-6. PMID:~~[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/9235893 9235893]~~

	~~IB1, a JIP-1-related nuclear protein present in insulin-secreting cells., Bonny C, Nicod P, Waeber G, J Biol Chem. 1998 Jan 23;273(4):1843-6.~~ PMID:~~[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/9442013 9442013]~~

	Recruitment of JNK to JIP1 and JNK-dependent JIP1 phosphorylation regulates JNK module dynamics and activation., Nihalani D, Wong HN, Holzman LB, J Biol Chem. 2003 Aug 1;278(31):28694-702. Epub 2003 May 19. PMID:~~[http://www.ncbi.nlm.nih.gov/pubmed~~/~~12756254 12756254]~~

	~~The JIP~~ group ~~of mitogen-activated protein kinase scaffold proteins., Yasuda J, Whitmarsh AJ, Cavanagh J, Sharma M, Davis RJ, Mol Cell Biol. 1999 Oct;19(10):7245-54.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/10490659 10490659]~~
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	~~[[Category: Single protein]]~~
	[[Category: Dar, I.]]		[[Category: Dar, I.]]
	[[Category: Gajhede, M.]]		[[Category: Gajhede, M.]]
Line 39:		Line 30:
	[[Category: All beta structure]]		[[Category: All beta structure]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 06~~:38:~~22 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:24:45 2009''