1ocy: Difference between revisions

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-[[Image:1ocy.png|left|200px]]
-<!--
+==Structure of the receptor-binding domain of the bacteriophage T4 short tail fibre==
-The line below this paragraph, containing "STRUCTURE_1ocy", creates the "Structure Box" on the page.
+<StructureSection load='1ocy' size='340' side='right'caption='[[1ocy]], [[Resolution|resolution]] 1.50&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'>[[1ocy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OCY 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]] 1.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1ocy|  PDB=1ocy  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ocy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ocy OCA], [https://pdbe.org/1ocy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ocy RCSB], [https://www.ebi.ac.uk/pdbsum/1ocy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ocy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FIB12_BPT4 FIB12_BPT4] Structural component of the short tail fiber. Adhesion protein that binds irreversibly to the lipopolysaccharides component (LPS) on the cell surface of Escherichia coli B strains during virus attachment. After at least three long tail fibers have bound, short tail fibers extend and bind irreversibly to the core region of the host cell LPS.<ref>PMID:12837775</ref>
+== 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/oc/1ocy_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=1ocy ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Adsorption of T4 bacteriophage to the Escherichia coli host cell is mediated by six long and six short tail fibres. After at least three long tail fibres have bound, short tail fibres extend and bind irreversibly to the core region of the host cell lipo-polysaccharide (LPS), serving as inextensible stays during penetration of the cell envelope by the tail tube. The short tail fibres consist of a parallel, in-register, trimer of gene product 12 (gp12).X-ray crystallography at 1.5A resolution of a protease-stable fragment of gp12 generated in the presence of zinc chloride reveals the structure of the C-terminal receptor-binding domain. It has a novel "knitted" fold, consisting of three extensively intertwined monomers. It reveals a metal-binding site, containing a zinc ion coordinated by six histidine residues in an octahedral conformation. We also suggest an LPS-binding region.
-===STRUCTURE OF THE RECEPTOR-BINDING DOMAIN OF THE BACTERIOPHAGE T4 SHORT TAIL FIBRE===
+The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold.,Thomassen E, Gielen G, Schutz M, Schoehn G, Abrahams JP, Miller S, van Raaij MJ J Mol Biol. 2003 Aug 8;331(2):361-73. PMID:12888344<ref>PMID:12888344</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_12888344}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ocy" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12888344 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12888344}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus T4]]
-[[1ocy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCY OCA].
+[[Category: Large Structures]]
+[[Category: Gielen G]]
-==Reference==
+[[Category: Miller S]]
-<ref group="xtra">PMID:12888344</ref><ref group="xtra">PMID:11743729</ref><ref group="xtra">PMID:11530935</ref><ref group="xtra">PMID:10782996</ref><ref group="xtra">PMID:10504409</ref><references group="xtra"/>
+[[Category: Schuetz M]]
-[[Category: Enterobacteria phage t4]]
+[[Category: Thomassen E]]
-[[Category: Gielen, G.]]
+[[Category: Van Raaij MJ]]
-[[Category: Miller, S.]]
-[[Category: Raaij, M J.Van.]]
-[[Category: Schuetz, M.]]
-[[Category: Thomassen, E.]]
-[[Category: Bacteriophage structural protein]]
-[[Category: Baseplate protein]]
-[[Category: Fibrous protein]]
-[[Category: Gene product 12]]
-[[Category: Lipo-polysaccharide binding]]
-[[Category: Structural protein]]