3cpj: Difference between revisions

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-{{Seed}}
-[[Image:3cpj.png|left|200px]]
-<!--
+==Crystal structure of Ypt31 in complex with yeast Rab-GDI==
-The line below this paragraph, containing "STRUCTURE_3cpj", creates the "Structure Box" on the page.
+<StructureSection load='3cpj' size='340' side='right'caption='[[3cpj]], [[Resolution|resolution]] 2.35&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'>[[3cpj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CPJ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_3cpj|  PDB=3cpj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cpj OCA], [https://pdbe.org/3cpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cpj RCSB], [https://www.ebi.ac.uk/pdbsum/3cpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cpj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GDI1_YEAST GDI1_YEAST] Regulates the GDP/GTP exchange reaction of SEC4 by inhibiting the dissociation of GDP from it, and the subsequent binding of GTP to SEC4. Plays an essential role in the yeast secretory pathway.<ref>PMID:8157010</ref>
+== 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/cp/3cpj_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/main_output.php?pdb_ID=3cpj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rab GDP dissociation inhibitors (GDI)-facilitated extraction of prenylated Rab proteins from membranes plays an important role in vesicular membrane trafficking. The investigated thermodynamic properties of yeast Rab.GDI and Rab.MRS6 complexes demonstrated differences in the Rab binding properties of the closely related Rab GDI and MRS6 proteins, consistent with their functional diversity. The importance of the Rab C terminus and its prenylation for GDI/MRS6 binding was demonstrated using both biochemical and structural data. The presented structures of the apo-form yeast Rab GDI and its two complexes with unprenylated Rab proteins, together with the earlier published structures of the prenylated Ypt1.GDI, provide evidence of allosteric regulation of the GDI lipid binding site opening, which plays a key role in the proposed mechanism of GDI-mediated Rab extraction. We suggest a model for the interaction of GDI with prenylated Rab proteins that incorporates a stepwise increase in affinity as the three different partial interactions are successively formed.
-===Crystal structure of Ypt31 in complex with yeast Rab-GDI===
+A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.,Ignatev A, Kravchenko S, Rak A, Goody RS, Pylypenko O J Biol Chem. 2008 Jun 27;283(26):18377-84. Epub 2008 Apr 20. PMID:18426803<ref>PMID:18426803</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3cpj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18426803}}, adds the Publication Abstract to the page
+*[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18426803 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18426803}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CPJ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CPJ OCA].
-==Reference==
-<ref group="xtra">PMID:18426803</ref><references group="xtra"/>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Goody, R S.]]
+[[Category: Goody RS]]
-[[Category: Ignatev, A.]]
+[[Category: Ignatev A]]
-[[Category: Kravchenko, S.]]
+[[Category: Kravchenko S]]
-[[Category: Pylypenko, O.]]
+[[Category: Pylypenko O]]
-[[Category: Rak, A.]]
+[[Category: Rak A]]
-[[Category: Acetylation]]
-[[Category: Cytoplasm]]
-[[Category: Golgi apparatus]]
-[[Category: Gtp-binding]]
-[[Category: Gtpase activation]]
-[[Category: Lipoprotein]]
-[[Category: Membrane]]
-[[Category: Nucleotide-binding]]
-[[Category: Phosphoprotein]]
-[[Category: Prenylation]]
-[[Category: Protein transport]]
-[[Category: Rab gtpase]]
-[[Category: Vesicular transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:23:04 2009''