2fpd: Difference between revisions

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[[Image:2fpd.png|left|200px]]


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==Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein==
The line below this paragraph, containing "STRUCTURE_2fpd", creates the "Structure Box" on the page.
<StructureSection load='2fpd' size='340' side='right'caption='[[2fpd]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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<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>
{{STRUCTURE_2fpd|  PDB=2fpd  |  SCENE=  }}
<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>
== 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).
== 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/initialview03.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/main_output.php?pdb_ID=2fpd 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.


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


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2fpd" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 16456539 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_16456539}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[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==
<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"/>
[[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: Signaling protein]]

Latest revision as of 12:07, 6 November 2024

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

Structural highlights

2fpd is a 4 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. 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. A unique set of SH3-SH3 interactions controls IB1 homodimerization. EMBO J. 2006 Feb 22;25(4):785-97. Epub 2006 Feb 2. PMID:16456539

2fpd, resolution 2.05Å

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