2pv9: Difference between revisions

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-{{Seed}}
-[[Image:2pv9.png|left|200px]]
-<!--
+==Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4==
-The line below this paragraph, containing "STRUCTURE_2pv9", creates the "Structure Box" on the page.
+<StructureSection load='2pv9' size='340' side='right'caption='[[2pv9]], [[Resolution|resolution]] 3.50&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'>[[2pv9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PV9 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]] 3.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_2pv9|  PDB=2pv9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pv9 OCA], [https://pdbe.org/2pv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pv9 RCSB], [https://www.ebi.ac.uk/pdbsum/2pv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pv9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/THRB_MOUSE THRB_MOUSE] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing (By similarity).
+== 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/pv/2pv9_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=2pv9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+It has been proposed that the cleaved form of protease-activated receptor 3 (PAR3) acts as a cofactor for thrombin cleavage and activation of PAR4 on murine platelets, but the molecular basis of this physiologically important effect remains elusive. X-ray crystal structures of murine thrombin bound to extracellular fragments of the murine receptors PAR3 ((38)SFNGGPQNTFEEFPLSDIE(56)) and PAR4 ((51)KSSDKPNPR downward arrow GYPGKFCANDSDTLELPASSQA(81), downward arrow = site of cleavage) have been solved at 2.0 and 3.5 A resolution, respectively. The cleaved form of PAR3, traced in the electron density maps from Gln-44 to Glu-56, makes extensive hydrophobic and electrostatic contacts with exosite I of thrombin through the fragment (47)FEEFPLSDIE(56). Occupancy of exosite I by PAR3 allosterically changes the conformation of the 60-loop and shifts the position of Trp-60d approximately 10 A with a resulting widening of the access to the active site. The PAR4 fragment, traced entirely in the electron density maps except for five C-terminal residues, clamps Trp-60d, Tyr-60a, and the aryl-binding site of thrombin with Pro-56 and Pro-58 at the P2 and P4 positions and engages the primary specificity pocket with Arg-59. The fragment then leaves the active site with Gly-60 and folds into a short helical turn that directs the backbone away from exosite I and over the autolysis loop. The structures demonstrate that thrombin activation of PAR4 may occur with exosite I available to bind cofactor molecules, like the cleaved form of PAR3, whose function is to promote substrate diffusion into the active site by allosterically changing the conformation of the 60-loop.
-===Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4===
+Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.,Bah A, Chen Z, Bush-Pelc LA, Mathews FS, Di Cera E Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11603-8. Epub 2007 Jul 2. PMID:17606903<ref>PMID:17606903</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2pv9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17606903}}, adds the Publication Abstract to the page
+*[[Thrombin 3D Structures|Thrombin 3D Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17606903 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17606903}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-PV9 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PV9 OCA].
-==Reference==
-Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4., Bah A, Chen Z, Bush-Pelc LA, Mathews FS, Di Cera E, Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11603-8. Epub 2007 Jul 2. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17606903 17606903]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
+[[Category: Bah A]]
-[[Category: Bah, A.]]
+[[Category: Bush-Pelc LA]]
-[[Category: Bush-Pelc, L A.]]
+[[Category: Chen Z]]
-[[Category: Cera, E Di.]]
+[[Category: Di Cera E]]
-[[Category: Chen, Z.]]
+[[Category: Mathews FS]]
-[[Category: Mathews, F S.]]
-[[Category: Serine protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:22:10 2008''