2nty: Difference between revisions

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-{{Seed}}
-[[Image:2nty.png|left|200px]]
-<!--
+==Rop4-GDP-PRONE8==
-The line below this paragraph, containing "STRUCTURE_2nty", creates the "Structure Box" on the page.
+<StructureSection load='2nty' size='340' side='right'caption='[[2nty]], [[Resolution|resolution]] 3.10&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'>[[2nty]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NTY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NTY 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]] 3.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-{{STRUCTURE_2nty|  PDB=2nty  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nty OCA], [https://pdbe.org/2nty PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nty RCSB], [https://www.ebi.ac.uk/pdbsum/2nty PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nty ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RAC5_ARATH RAC5_ARATH] May be involved in cell polarity control during the actin-dependent tip growth of root hairs.<ref>PMID:11387211</ref>   Inactive GDP-bound Rho GTPases reside in the cytosol, are found in a complex with Rho GDP-dissociation inhibitors (Rho GDIs), and are released from the GDI protein in order to translocate to membranes upon activation.<ref>PMID:11387211</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/nt/2nty_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=2nty ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rho of plants (Rop) proteins belong to the superfamily of small GTP-binding (G) proteins and are vital regulators of signal transduction in plants. In order to become activated, Rop proteins need to exchange GDP for GTP, an intrinsically slow process catalyzed by guanine nucleotide exchange factors (GEFs). RopGEFs show no homology to animal RhoGEFs, and the catalytic mechanism remains elusive. GEF-catalysed nucleotide exchange proceeds via transient ternary and stable binary complexes. While a number of structural studies have analyzed binary nucleotide-free G protein-GEF complexes, very little is known about the ternary complexes. Here we report the X-ray structure of the catalytic PRONE domain of RopGEF8 from Arabidopsis thaliana, both alone and in a ternary complex with Rop4 and GDP. The features of the latter complex, a transient intermediate of the exchange reaction never directly observed before, suggest a common mechanism of catalyzed nucleotide exchange applicable to small G proteins in general.
-===Rop4-GDP-PRONE8===
+Structural evidence for a common intermediate in small G protein-GEF reactions.,Thomas C, Fricke I, Scrima A, Berken A, Wittinghofer A Mol Cell. 2007 Jan 12;25(1):141-9. PMID:17218277<ref>PMID:17218277</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2nty" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17218277}}, 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 17218277 is the PubMed ID number.
+*[[Rho guanine nucleotide exchange factor 3D structures|Rho guanine nucleotide exchange factor 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_17218277}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-NTY is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NTY OCA].
-==Reference==
-Structural evidence for a common intermediate in small G protein-GEF reactions., Thomas C, Fricke I, Scrima A, Berken A, Wittinghofer A, Mol Cell. 2007 Jan 12;25(1):141-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17218277 17218277]
-Purification and crystallization of the catalytic PRONE domain of RopGEF8 and its complex with Rop4 from Arabidopsis thaliana., Thomas C, Weyand M, Wittinghofer A, Berken A, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jun 1;62(Pt, 6):607-10. Epub 2006 May 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16754995 16754995]
 [[Category: Arabidopsis thaliana]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Berken, A.]]
+[[Category: Berken A]]
-[[Category: Fricke, I.]]
+[[Category: Fricke I]]
-[[Category: Scrima, A.]]
+[[Category: Scrima A]]
-[[Category: Thomas, C.]]
+[[Category: Thomas C]]
-[[Category: Wittinghofer, A.]]
+[[Category: Wittinghofer A]]
-[[Category: Complex of prone-gef with rop substrate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 12:18:54 2008''