2kri: Difference between revisions

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-{{STRUCTURE_2kri|  PDB=2kri  |  SCENE=  }}
-===Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock===
-{{ABSTRACT_PUBMED_20223219}}
-==Disease==
+==Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock==
-[[http://www.uniprot.org/uniprot/LDLR_HUMAN LDLR_HUMAN]] Defects in LDLR are the cause of familial hypercholesterolemia (FH) [MIM:[http://omim.org/entry/143890 143890]]; a common autosomal semi-dominant disease that affects about 1 in 500 individuals. The receptor defect impairs the catabolism of LDL, and the resultant elevation in plasma LDL-cholesterol promotes deposition of cholesterol in the skin (xanthelasma), tendons (xanthomas), and coronary arteries (atherosclerosis).<ref>PMID:3263645</ref><ref>PMID:2569482</ref><ref>PMID:3955657</ref><ref>PMID:8347689</ref><ref>PMID:2318961</ref><ref>PMID:1446662</ref><ref>PMID:1867200</ref><ref>PMID:8462973</ref><ref>PMID:8168830</ref><ref>PMID:2726768</ref><ref>PMID:1464748</ref><ref>PMID:7573037</ref><ref>PMID:7583548</ref><ref>PMID:7550239</ref><ref>PMID:7635461</ref><ref>PMID:7635482</ref><ref>PMID:7649546</ref><ref>PMID:7649549</ref><ref>PMID:8740918</ref><ref>PMID:8664907</ref><ref>PMID:9026534</ref><ref>PMID:9254862</ref><ref>PMID:9143924</ref><ref>PMID:9259195</ref><ref>PMID:9104431</ref><ref>PMID:9654205</ref><ref>PMID:9452094</ref><ref>PMID:9452095</ref><ref>PMID:9452118</ref><ref>PMID:10206683</ref><ref>PMID:10660340</ref>[:]<ref>PMID:9852677</ref><ref>PMID:9678702</ref><ref>PMID:10422803</ref><ref>PMID:10090484</ref><ref>PMID:10447263</ref><ref>PMID:10978268</ref><ref>PMID:10980548</ref><ref>PMID:10882754</ref><ref>PMID:11298688</ref><ref>PMID:17142622</ref><ref>PMID:19319977</ref><ref>PMID:22160468</ref>
+<StructureSection load='2kri' size='340' side='right'caption='[[2kri]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2kri]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KRI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KRI FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 1 model</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=2kri FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kri OCA], [https://pdbe.org/2kri PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kri RCSB], [https://www.ebi.ac.uk/pdbsum/2kri PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kri ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/APOH_HUMAN APOH_HUMAN] Binds to various kinds of negatively charged substances such as heparin, phospholipids, and dextran sulfate. May prevent activation of the intrinsic blood coagulation cascade by binding to phospholipids on the surface of damaged cells.
+== 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/kr/2kri_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=2kri ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Lipoprotein receptors of the LDLR family serve as clearance receptors for beta2GPI and as signaling receptors for the beta2GPI/antibody complexes in antiphospholipid syndrome. We compared four ligand-binding LA modules from LDLR and ApoER2 for their ability to bind domain V of beta2GPI (beta2GPI-DV). We found that the LA modules capable of binding beta2GPI-DV interact with the same region on beta2GPI-DV using residues at their calcium-coordination site. The structure of a complex between beta2GPI-DV and LA4 of LDLR, solved by molecular docking guided by NMR-derived restraints and extensively validated, represents the general mode of interaction between beta2GPI and lipoprotein receptors. We have shown that beta2GPI-DV cannot simultaneously bind to lipoprotein receptors and anionic phospholipids, suggesting that the association of beta2GPI/anti-beta2GPI antibody complexes with anionic phospholipids will interfere with lipoprotein receptors' signaling in APS.
-==Function==
+Mode of interaction between beta2GPI and lipoprotein receptors suggests mutually exclusive binding of beta2GPI to the receptors and anionic phospholipids.,Lee CJ, De Biasio A, Beglova N Structure. 2010 Mar 10;18(3):366-76. PMID:20223219<ref>PMID:20223219</ref>
-[[http://www.uniprot.org/uniprot/APOH_HUMAN APOH_HUMAN]] Binds to various kinds of negatively charged substances such as heparin, phospholipids, and dextran sulfate. May prevent activation of the intrinsic blood coagulation cascade by binding to phospholipids on the surface of damaged cells. [[http://www.uniprot.org/uniprot/LDLR_HUMAN LDLR_HUMAN]] Binds LDL, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. In case of HIV-1 infection, functions as a receptor for extracellular Tat in neurons, mediating its internalization in uninfected cells.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[2kri]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KRI OCA].
+</div>
+<div class="pdbe-citations 2kri" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-<ref group="xtra">PMID:020223219</ref><references group="xtra"/><references/>
+*[[LDL receptor|LDL receptor]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Beglova, N.]]
+[[Category: Large Structures]]
-[[Category: Antiphospholipid syndrome]]
+[[Category: Beglova N]]
-[[Category: Disulfide bond]]
-[[Category: Glycoprotein]]
-[[Category: Heparin-binding]]
-[[Category: Ldlr]]
-[[Category: Protein binding-endocytosis complex]]
-[[Category: Receptor]]
-[[Category: Sushi]]
-[[Category: Thrombosis]]