3par: Difference between revisions

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-[[Image:3par.png|left|200px]]
-<!--
+==Surfactant Protein-A neck and carbohydrate recognition domain (NCRD) in the absence of ligand==
-The line below this paragraph, containing "STRUCTURE_3par", creates the "Structure Box" on the page.
+<StructureSection load='3par' size='340' side='right'caption='[[3par]], [[Resolution|resolution]] 2.30&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'>[[3par]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PAR 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]] 2.3&#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>
-{{STRUCTURE_3par|  PDB=3par  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3par FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3par OCA], [https://pdbe.org/3par PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3par RCSB], [https://www.ebi.ac.uk/pdbsum/3par PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3par ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SFTPA_RAT SFTPA_RAT] In presence of calcium ions, it binds to surfactant phospholipids and contributes to lower the surface tension at the air-liquid interface in the alveoli of the mammalian lung and is essential for normal respiration.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Surfactant protein A (SP-A), a C-type lectin, plays an important role in innate lung host defense against inhaled pathogens. Crystallographic SP-A.ligand complexes have not been reported to date, limiting available molecular information about SP-A interactions with microbial surface components. This study describes crystal structures of calcium-dependent complexes of the C-terminal neck and carbohydrate recognition domain of SP-A with d-mannose, d-alpha-methylmannose, and glycerol, which represent subdomains of glycans on pathogen surfaces. Comparison of these complexes with the unliganded SP-A neck and carbohydrate recognition domain revealed an unexpected ligand-associated conformational change in the loop region surrounding the lectin site, one not previously reported for the lectin homologs SP-D and mannan-binding lectin. The net result of the conformational change is that the SP-A lectin site and the surrounding loop region become more compact. The Glu-202 side chain of unliganded SP-A extends out into the solvent and away from the calcium ion; however, in the complexes, the Glu-202 side chain translocates 12.8 A to bind the calcium. The availability of Glu-202, together with positional changes involving water molecules, creates a more favorable hydrogen bonding environment for carbohydrate ligands. The Lys-203 side chain reorients as well, extending outward into the solvent in the complexes, thereby opening up a small cation-friendly cavity occupied by a sodium ion. Binding of this cation brings the large loop, which forms one wall of the lectin site, and the adjacent small loop closer together. The ability to undergo conformational changes may help SP-A adapt to different ligand classes, including microbial glycolipids and surfactant lipids.
-===Surfactant Protein-A neck and carbohydrate recognition domain (NCRD) in the absence of ligand===
+Crystallographic Complexes of Surfactant Protein A and Carbohydrates Reveal Ligand-induced Conformational Change.,Shang F, Rynkiewicz MJ, McCormack FX, Wu H, Cafarella TM, Head JF, Seaton BA J Biol Chem. 2011 Jan 7;286(1):757-65. Epub 2010 Nov 3. PMID:21047777<ref>PMID:21047777</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_21047777}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3par" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21047777 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21047777}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3par]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PAR OCA].
-==Reference==
-<ref group="xtra">PMID:21047777</ref><references group="xtra"/>
 [[Category: Rattus norvegicus]]
-[[Category: Cafarella, T M.]]
+[[Category: Cafarella TM]]
-[[Category: Head, J.]]
+[[Category: Head J]]
-[[Category: McCormack, F X.]]
+[[Category: McCormack FX]]
-[[Category: Rynkiewicz, M J.]]
+[[Category: Rynkiewicz MJ]]
-[[Category: Seaton, B A.]]
+[[Category: Seaton BA]]
-[[Category: Shang, F.]]
+[[Category: Shang F]]
-[[Category: Wu, H.]]
+[[Category: Wu H]]