1z40: Difference between revisions

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-{{Seed}}
-[[Image:1z40.png|left|200px]]
-<!--
+==AMA1 from Plasmodium falciparum==
-The line below this paragraph, containing "STRUCTURE_1z40", creates the "Structure Box" on the page.
+<StructureSection load='1z40' size='340' side='right'caption='[[1z40]], [[Resolution|resolution]] 1.90&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'>[[1z40]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum_3D7 Plasmodium falciparum 3D7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z40 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]] 1.901&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-{{STRUCTURE_1z40|  PDB=1z40  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z40 OCA], [https://pdbe.org/1z40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z40 RCSB], [https://www.ebi.ac.uk/pdbsum/1z40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z40 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7KQK5_PLAF7 Q7KQK5_PLAF7]
+== 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/z4/1z40_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=1z40 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Apical membrane antigen 1 (AMA1) is a leading malaria vaccine candidate that possesses polymorphisms that may pose a problem for a vaccine based on this antigen. Knowledge of the distribution of the polymorphic sites on the surface of AMA1 is necessary to obtain a detailed understanding of their significance for vaccine development. For this reason we have sought to determine the three-dimensional structure of AMA1 using x-ray crystallography. The central two-thirds of AMA1 is relatively conserved among Plasmodium species as well as more distantly related apicomplexan parasites, and contains two clusters of disulfide-bonded cysteines termed domains I and II. The crystal structure of this fragment of AMA1 reported here reveals that domains I+II consists of two intimately associated PAN domains. PAN domain I contains many long loops that extend from the domain core and form a scaffold for numerous polymorphic residues. This extreme adaptation of a PAN domain reveals how malaria parasites have introduced significant flexibility and variation into AMA1 to evade protective human antibody responses. The polymorphisms on the AMA1 surface are exclusively located on one side of the molecule, presumably because this region of AMA1 is most accessible to antibodies reacting with the parasite surface. Moreover, the most highly polymorphic residues surround a conserved hydrophobic trough that is ringed by domain I and domain II loops. Precedents set by viral receptor proteins would suggest that this is likely to be the AMA1 receptor binding pocket.
-===AMA1 from Plasmodium falciparum===
+Structure of AMA1 from Plasmodium falciparum reveals a clustering of polymorphisms that surround a conserved hydrophobic pocket.,Bai T, Becker M, Gupta A, Strike P, Murphy VJ, Anders RF, Batchelor AH Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12736-41. Epub 2005 Aug 29. PMID:16129835<ref>PMID:16129835</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16129835}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1z40" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16129835 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16129835}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Z40 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Plasmodium_falciparum_3d7 Plasmodium falciparum 3d7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z40 OCA].
+[[Category: Plasmodium falciparum 3D7]]
+[[Category: Anders RF]]
-==Reference==
+[[Category: Bai T]]
-<ref group="xtra">PMID:16129835</ref><references group="xtra"/>
+[[Category: Batchelor AH]]
-[[Category: Plasmodium falciparum 3d7]]
+[[Category: Becker M]]
-[[Category: Anders, R F.]]
+[[Category: Gupta A]]
-[[Category: Bai, T.]]
+[[Category: Murphy VJ]]
-[[Category: Batchelor, A H.]]
+[[Category: Strike P]]
-[[Category: Becker, M.]]
-[[Category: Gupta, A.]]
-[[Category: Murphy, V J.]]
-[[Category: Strike, P.]]
-[[Category: Malaria vaccine candidate]]
-[[Category: Pan or apple domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:50:50 2009''