1rl0: Difference between revisions

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-{{Seed}}
-[[Image:1rl0.png|left|200px]]
-<!--
+==Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30==
-The line below this paragraph, containing "STRUCTURE_1rl0", creates the "Structure Box" on the page.
+<StructureSection load='1rl0' size='340' side='right'caption='[[1rl0]], [[Resolution|resolution]] 1.40&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'>[[1rl0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dianthus_caryophyllus Dianthus caryophyllus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RL0 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]] 1.4&#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=1rl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rl0 OCA], [https://pdbe.org/1rl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rl0 RCSB], [https://www.ebi.ac.uk/pdbsum/1rl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rl0 ProSAT]</span></td></tr>
-{{STRUCTURE_1rl0|  PDB=1rl0  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIP0_DIACA RIP0_DIACA] Single-chain ribosome-inactivating protein.
+== 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/rl/1rl0_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=1rl0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribosome inactivating proteins (RIPs) are plant proteins with enzymatic activity identified as rRNA N-glycosidase (EC 3.2.2.22), which cleaves the N-glycosidic bond of a specific adenine on the ricin/sarcin region of rRNA, thus causing inhibition of protein synthesis. They also depurinate extensively DNA and other polynucleotides. The three-dimensional structure of dianthin 30, a type 1 (single-chain) RIP of Dianthus caryophyllus (leaves), is now described at 1.4 angstroms, a resolution never achieved before for any RIP. The fold typical of RIPs is conserved, despite some differences in the loop regions. The general structure comparison by superimposed alpha-carbon (249 atoms) and the sequence alignment by structure for dianthin 30 and saporin-S6 give a root mean square deviation of 0.625 angstroms. Despite the differences reported for the biological activities of the two RIPs, their structures fit quite well and both show a protein segment containing strands beta7, beta8, and beta9 shorter than other RIPs. However, the surface electrostatic potential in the active site region neatly distinguishes dianthin 30 from saporin-S6. The possible relationship between the charge distribution and the behavior of the proteins toward different substrates is discussed.
-===Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30===
+The 1.4 anstroms structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins.,Fermani S, Falini G, Ripamonti A, Polito L, Stirpe F, Bolognesi A J Struct Biol. 2005 Feb;149(2):204-12. PMID:15681236<ref>PMID:15681236</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1rl0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15681236}}, adds the Publication Abstract to the page
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15681236 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15681236}}
+__TOC__
+</StructureSection>
-==About this Structure==
-RL0 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Dianthus_caryophyllus Dianthus caryophyllus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RL0 OCA].
-==Reference==
-<ref group="xtra">PMID:15681236</ref><references group="xtra"/>
 [[Category: Dianthus caryophyllus]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Large Structures]]
-[[Category: Bolognesi, A.]]
+[[Category: Bolognesi A]]
-[[Category: Falini, G.]]
+[[Category: Falini G]]
-[[Category: Fermani, S.]]
+[[Category: Fermani S]]
-[[Category: Polito, L.]]
+[[Category: Polito L]]
-[[Category: Ripamonti, A.]]
+[[Category: Ripamonti A]]
-[[Category: Stirpe, F.]]
+[[Category: Stirpe F]]
-[[Category: Alpha and beta region]]
-[[Category: Mixed beta-sheet]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:43:46 2009''