1avr: Difference between revisions

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-[[Image:1avr.gif|left|200px]]<br />
-<applet load="1avr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1avr, resolution 2.3&Aring;" />
-'''CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS'''<br />
-==Overview==
+==CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS==
-Two crystal forms (P6(3) and R3) of human annexin V have been, crystallographically refined at 2.3 A and 2.0 A resolution to R-values of, 0.184 and 0.174, respectively, applying very tight stereochemical, restraints with deviations from ideal geometry of 0.01 A and 2 degrees., The three independent molecules (2 in P6(3), 1 in R3) are similar, with, deviations in C alpha positions of 0.6 A. The polypeptide chain of 320, amino acid residues is folded into a planar cyclic arrangement of four, repeats. The repeats have similar structures of five alpha-helical, segments wound into a right-handed compact superhelix. Three calcium ion, sites in repeats I, II and IV and two lanthanum ion sites in repeat I have, been found in the R3 crystals. They are located at the convex face of the, molecule opposite the N terminus. Repeat III has a different conformation, at this site and no calcium bound. The calcium sites are similar to the, phospholipase A2 calcium-binding site, suggesting analogy also in, phospholipid interaction. The center of the molecule is formed by a, channel of polar charged residues, which also harbors a chain of ordered, water molecules conserved in the different crystal forms. Comparison with, amino acid sequences of other annexins shows a high degree of similarity, between them. Long insertions are found only at the N termini. Most, conserved are the residues forming the metal-binding sites and the polar, channel. Annexins V and VII form voltage-gated calcium ion channels when, bound to membranes in vitro. We suggest that annexins bind with their, convex face to membranes, causing local disorder and permeability of the, phospholipid bilayers. Annexins are Janus-faced proteins that face, phospholipid and water and mediate calcium transport.
+<StructureSection load='1avr' size='340' side='right'caption='[[1avr]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1avr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AVR 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]] 2.3&#8491;</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1avr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1avr OCA], [https://pdbe.org/1avr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1avr RCSB], [https://www.ebi.ac.uk/pdbsum/1avr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1avr ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/ANXA5_HUMAN ANXA5_HUMAN] Defects in ANXA5 are associated with susceptibility to pregnancy loss, recurrent, type 3 (RPRGL3) [MIM:[https://omim.org/entry/614391 614391]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:17339269</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/ANXA5_HUMAN ANXA5_HUMAN] This protein is an anticoagulant protein that acts as an indirect inhibitor of the thromboplastin-specific complex, which is involved in the blood coagulation cascade.
+== 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/av/1avr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1avr ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-AVR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with CA and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AVR OCA].
+*[[Annexin 3D structures|Annexin 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal and molecular structure of human annexin V after refinement. Implications for structure, membrane binding and ion channel formation of the annexin family of proteins., Huber R, Berendes R, Burger A, Schneider M, Karshikov A, Luecke H, Romisch J, Paques E, J Mol Biol. 1992 Feb 5;223(3):683-704. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1311770 1311770]
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Berendes, R.]]
+[[Category: Berendes R]]
-[[Category: Burger, A.]]
+[[Category: Burger A]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Karshikov, A.]]
+[[Category: Karshikov A]]
-[[Category: Luecke, H.]]
+[[Category: Luecke H]]
-[[Category: Paques, E.]]
+[[Category: Paques E]]
-[[Category: Roemisch, J.]]
+[[Category: Roemisch J]]
-[[Category: Schneider, M.]]
+[[Category: Schneider M]]
-[[Category: CA]]
-[[Category: SO4]]
-[[Category: calcium/phospholipid binding]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 16:02:41 2007''