1z40: Difference between revisions

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-[[Image:1z40.png|left|200px]]
-{{STRUCTURE_1z40|  PDB=1z40  |  SCENE=  }}
+==AMA1 from Plasmodium falciparum==
+<StructureSection load='1z40' size='340' side='right'caption='[[1z40]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
-{{ABSTRACT_PUBMED_16129835}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1z40" style="background-color:#fffaf0;"></div>
-[[1z40]] is a 2 chain structure with sequence 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].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:016129835</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Plasmodium falciparum 3d7]]
+[[Category: Large Structures]]
-[[Category: Anders, R F.]]
+[[Category: Plasmodium falciparum 3D7]]
-[[Category: Bai, T.]]
+[[Category: Anders RF]]
-[[Category: Batchelor, A H.]]
+[[Category: Bai T]]
-[[Category: Becker, M.]]
+[[Category: Batchelor AH]]
-[[Category: Gupta, A.]]
+[[Category: Becker M]]
-[[Category: Murphy, V J.]]
+[[Category: Gupta A]]
-[[Category: Strike, P.]]
+[[Category: Murphy VJ]]
-[[Category: Malaria vaccine candidate]]
+[[Category: Strike P]]
-[[Category: Pan or apple domain]]
-[[Category: Unknown function]]