2ifu: Difference between revisions

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-{{Seed}}
-[[Image:2ifu.png|left|200px]]
-<!--
+==Crystal Structure of a Gamma-SNAP from Danio rerio==
-The line below this paragraph, containing "STRUCTURE_2ifu", creates the "Structure Box" on the page.
+<StructureSection load='2ifu' size='340' side='right'caption='[[2ifu]], [[Resolution|resolution]] 2.60&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'>[[2ifu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IFU FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2ifu|  PDB=2ifu  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">zgc:110177 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=2ifu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ifu OCA], [https://pdbe.org/2ifu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ifu RCSB], [https://www.ebi.ac.uk/pdbsum/2ifu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ifu ProSAT], [https://www.topsan.org/Proteins/CESG/2ifu TOPSAN]</span></td></tr>
+</table>
+== 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/if/2ifu_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=2ifu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Soluble N-ethylmaleimide-sensitive factor attachment protein gamma (gamma-SNAP) is a member of an eukaryotic protein family involved in intracellular membrane trafficking. The X-ray structure of Brachydanio rerio gamma-SNAP was determined to 2.6 A and revealed an all-helical protein comprised of an extended twisted-sheet of helical hairpins with a helical-bundle domain on its carboxy-terminal end. Structural and conformational differences between multiple observed gamma-SNAP molecules and Sec17, a SNAP family protein from yeast, are analyzed. Conformational variation in gamma-SNAP molecules is matched with great precision by the two lowest frequency normal modes of the structure. Comparison of the lowest-frequency modes from gamma-SNAP and Sec17 indicated that the structures share preferred directions of flexibility, corresponding to bending and twisting of the twisted sheet motif. We discuss possible consequences related to the flexibility of the SNAP proteins for the mechanism of the 20S complex disassembly during the SNAP receptors recycling.
-===Crystal Structure of a Gamma-SNAP from Danio rerio===
+Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family.,Bitto E, Bingman CA, Kondrashov DA, McCoy JG, Bannen RM, Wesenberg GE, Phillips GN Jr Proteins. 2008 Jan 1;70(1):93-104. PMID:17634982<ref>PMID:17634982</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_17634982}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ifu" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17634982 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17634982}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Brachidanio rerio]]
-IFU is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IFU OCA].
+[[Category: Large Structures]]
+[[Category: Bingman, C A]]
-==Reference==
+[[Category: Bitto, E]]
-<ref group="xtra">PMID:17634982</ref><references group="xtra"/>
+[[Category: Structural genomic]]
-[[Category: Danio rerio]]
+[[Category: Mccoy, J G]]
-[[Category: Bingman, C A.]]
+[[Category: Phillips, G N]]
-[[Category: Bitto, E.]]
+[[Category: Wesenberg, G E]]
-[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
-[[Category: Jr., G N.Phillips.]]
-[[Category: Mccoy, J G.]]
-[[Category: Wesenberg, G E.]]
-[[Category: Center for eukaryotic structural genomic]]
 [[Category: Cesg]]
-[[Category: Endocytosis/exocytosis complex]]
+[[Category: Endocytosis-exocytosis complex]]
 [[Category: Gamma-snap]]
 [[Category: Membrane fusion]]
-[[Category: Protein structure initiative]]
+[[Category: PSI, Protein structure initiative]]
-[[Category: Psi]]
 [[Category: Snare complex disassembly]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 01:07:24 2009''