3ckd: Difference between revisions

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-[[Image:3ckd.jpg|left|200px]]
- {{Structure
+==Crystal structure of the C-terminal domain of the Shigella type III effector IpaH==
-|PDB= 3ckd |SIZE=350|CAPTION= <scene name='initialview01'>3ckd</scene>, resolution 2.65&Aring;
+<StructureSection load='3ckd' size='340' side='right'caption='[[3ckd]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+C+600'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+B+601'>AC2</scene>, <scene name='pdbsite=AC3:Gol+Binding+Site+For+Residue+C+602'>AC3</scene>, <scene name='pdbsite=AC4:Gol+Binding+Site+For+Residue+C+603'>AC4</scene>, <scene name='pdbsite=AC5:Gol+Binding+Site+For+Residue+C+604'>AC5</scene> and <scene name='pdbsite=AC6:Peg+Binding+Site+For+Residue+C+605'>AC6</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[3ckd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri_2a_str._301 Shigella flexneri 2a str. 301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CKD FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
-|GENE= ipaH1.4, CP0265 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198214 Shigella flexneri 2a str. 301])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG4886 COG4886]</span>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ckd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckd OCA], [https://pdbe.org/3ckd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ckd RCSB], [https://www.ebi.ac.uk/pdbsum/3ckd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ckd ProSAT], [https://www.topsan.org/Proteins/MCSG/3ckd TOPSAN]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ckd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckd OCA], [http://www.ebi.ac.uk/pdbsum/3ckd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3ckd RCSB]</span>
+== 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/ck/3ckd_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=3ckd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+IpaH proteins are E3 ubiquitin ligases delivered by the type III secretion apparatus into host cells upon infection of humans by the Gram-negative pathogen Shigella flexneri. These proteins comprise a variable leucine-rich repeat-containing N-terminal domain and a conserved C-terminal domain harboring an invariant cysteine residue that is crucial for activity. IpaH homologs are encoded by diverse animal and plant pathogens. Here we demonstrate that the IpaH C-terminal domain carries the catalytic activity for ubiquitin transfer and that the N-terminal domain carries the substrate specificity. The structure of the IpaH C-terminal domain, determined to 2.65-A resolution, represents an all-helical fold bearing no resemblance to previously defined E3 ubiquitin ligases. The conserved and essential cysteine residue lies on a flexible, surface-exposed loop surrounded by conserved acidic residues, two of which are crucial for IpaH activity.
-'''Crystal structure of the C-terminal domain of the Shigella type III effector IpaH'''
+Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.,Singer AU, Rohde JR, Lam R, Skarina T, Kagan O, Dileo R, Chirgadze NY, Cuff ME, Joachimiak A, Tyers M, Sansonetti PJ, Parsot C, Savchenko A Nat Struct Mol Biol. 2008 Dec;15(12):1293-301. Epub 2008 Nov 9. PMID:18997778<ref>PMID:18997778</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-CKD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri_2a_str._301 Shigella flexneri 2a str. 301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CKD OCA].
+<div class="pdbe-citations 3ckd" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Shigella flexneri 2a str. 301]]
-[[Category: Single protein]]
+[[Category: Cuff ME]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: DiLeo R]]
-[[Category: Cuff, M E.]]
+[[Category: Edwards AM]]
-[[Category: DiLeo, R.]]
+[[Category: Joachimiak A]]
-[[Category: Edwards, A M.]]
+[[Category: Kagan O]]
-[[Category: Joachimiak, A.]]
+[[Category: Lam R]]
-[[Category: Kagan, O.]]
+[[Category: Savchenko A]]
-[[Category: Lam, R.]]
+[[Category: Singer AU]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Skarina T]]
-[[Category: Savchenko, A.]]
-[[Category: Singer, A U.]]
-[[Category: Skarina, T.]]
-[[Category: e3 ubiquitin ligase]]
-[[Category: helical]]
-[[Category: mcsg]]
-[[Category: midwest center for structural genomic]]
-[[Category: plasmid]]
-[[Category: protein structure initiative]]
-[[Category: psi-2]]
-[[Category: structural genomic]]
-[[Category: type iii effector]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:32:33 2008''