2zr1: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2zr1.png|left|200px]]
-<!--
+==Agglutinin from Abrus Precatorius==
-The line below this paragraph, containing "STRUCTURE_2zr1", creates the "Structure Box" on the page.
+<StructureSection load='2zr1' size='340' side='right'caption='[[2zr1]], [[Resolution|resolution]] 2.60&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'>[[2zr1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Abrus_precatorius Abrus precatorius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZR1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZR1 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_2zr1|  PDB=2zr1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zr1 OCA], [https://pdbe.org/2zr1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zr1 RCSB], [https://www.ebi.ac.uk/pdbsum/2zr1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zr1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AGGL_ABRPR AGGL_ABRPR] The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA (By similarity). Less toxic than abrin-a.<ref>PMID:10636890</ref> [UniProtKB:P28590]  The B chain is a galactose-specific lectin that facilitates the binding to the cell membrane that precedes endocytosis (By similarity).<ref>PMID:10636890</ref> [UniProtKB:P28590]
+== 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/zr/2zr1_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=2zr1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+X-ray crystal structure determination of agglutinin from Abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P4(1)2(1)2 with Z = 8, and been refined at 2.6 A to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 A and 1.3 degrees. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.
-===Agglutinin from Abrus Precatorius===
+A biophysical elucidation for less toxicity of agglutinin than abrin-a from the seeds of Abrus precatorius in consequence of crystal structure.,Cheng J, Lu TH, Liu CL, Lin JY J Biomed Sci. 2010 Apr 30;17:34. PMID:20433687<ref>PMID:20433687</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2zr1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20433687}}, adds the Publication Abstract to the page
+*[[Agglutinin 3D structures|Agglutinin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20433687 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20433687}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ZR1 is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Abrus_precatorius Abrus precatorius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZR1 OCA].
-==Reference==
-<ref group="xtra">PMID:20433687</ref><ref group="xtra">PMID:16772301</ref><ref group="xtra">PMID:10636890</ref><ref group="xtra">PMID:10930837</ref><ref group="xtra">PMID:7608980</ref><references group="xtra"/>
 [[Category: Abrus precatorius]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Large Structures]]
-[[Category: Cheng, J.]]
+[[Category: Cheng J]]
-[[Category: Lin, J Y.]]
+[[Category: Lin JY]]
-[[Category: Liu, C L.]]
+[[Category: Liu CL]]
-[[Category: Lu, T H.]]
+[[Category: Lu TH]]
-[[Category: Agglutinin abrin]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Immunotoxin]]
-[[Category: Lectin]]
-[[Category: Plant defense]]
-[[Category: Plant protein]]
-[[Category: Protein synthesis inhibitor]]
-[[Category: Pyrrolidone carboxylic acid]]
-[[Category: Ribosome-inactivating protein]]
-[[Category: Toxin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 20 09:09:29 2010''