2zr1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2zr1" [edit=sysop:move=sysop])
Current revision (08:42, 30 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[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==
+
-
[[2zr1]] is a 4 chain structure with sequence 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: 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]]
+

Current revision

Agglutinin from Abrus Precatorius

PDB ID 2zr1

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zr1"
Personal tools