2jdl: Difference between revisions

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-{{Seed}}
-[[Image:2jdl.png|left|200px]]
-<!--
+==Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin==
-The line below this paragraph, containing "STRUCTURE_2jdl", creates the "Structure Box" on the page.
+<StructureSection load='2jdl' size='340' side='right'caption='[[2jdl]], [[Resolution|resolution]] 2.20&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'>[[2jdl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Trichosanthes_kirilowii Trichosanthes kirilowii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JDL 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]] 2.2&#8491;</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=2jdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdl OCA], [https://pdbe.org/2jdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jdl RCSB], [https://www.ebi.ac.uk/pdbsum/2jdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jdl ProSAT]</span></td></tr>
-{{STRUCTURE_2jdl|  PDB=2jdl  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIPT_TRIKI RIPT_TRIKI] Inactivates eukaryotic 60S ribosomal subunits.
+== 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/jd/2jdl_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=2jdl ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of trichosanthin (TCS) complexed to the peptide SDDDMGFGLFD, which corresponds to the conserved C-terminal elongation factor binding domain of the ribosomal P protein. The N-terminal region of this peptide interacts with Lys173, Arg174 and Lys177 in TCS, while the C-terminal region is inserted into a hydrophobic pocket. The interaction with the P protein contributes to the ribosome-inactivating activity of TCS. This 11-mer C-terminal P peptide can be docked with selected important plant and bacterial RIPs, indicating that a similar interaction may also occur with other RIPs.
-===STRUCTURE OF C-TERMINAL REGION OF ACIDIC P2 RIBOSOMAL PROTEIN COMPLEXED WITH TRICHOSANTHIN===
+The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.,Too PH, Ma MK, Mak AN, Wong YT, Tung CK, Zhu G, Au SW, Wong KB, Shaw PC Nucleic Acids Res. 2009 Feb;37(2):602-10. Epub 2008 Dec 10. PMID:19073700<ref>PMID:19073700</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jdl" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19073700}}, adds the Publication Abstract to the page
+*[[Ribosomal protein P2|Ribosomal protein P2]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19073700 is the PubMed ID number.
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_19073700}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-JDL is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Trichosanthes_kirilowii Trichosanthes kirilowii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDL OCA].
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:19073700</ref><references group="xtra"/>
 [[Category: Trichosanthes kirilowii]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Au SW]]
-[[Category: Au, S W.]]
+[[Category: Mak AN]]
-[[Category: Mak, A N.]]
+[[Category: Shaw PC]]
-[[Category: Shaw, P C.]]
+[[Category: Too PH]]
-[[Category: Too, P H.]]
+[[Category: Wong KB]]
-[[Category: Wong, K B.]]
+[[Category: Zhu G]]
-[[Category: Zhu, G.]]
-[[Category: Antiviral protein]]
-[[Category: Hydrolase]]
-[[Category: Plant defense]]
-[[Category: Protein synthesis inhibitor]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome inactiviating protein]]
-[[Category: Toxin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 11:22:37 2009''