1pdl: Difference between revisions

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 ==Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate==
-<StructureSection load='1pdl' size='340' side='right' caption='[[1pdl]], [[Resolution|resolution]] 12.00&Aring;' scene=''>
+<SX load='1pdl' size='340' side='right' viewer='molstar' caption='[[1pdl]], [[Resolution|resolution]] 12.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pdl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PDL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pdl]] is a 3 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=1PDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PDL FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1k28|1k28]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 12&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></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=1pdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pdl OCA], [https://pdbe.org/1pdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pdl RCSB], [https://www.ebi.ac.uk/pdbsum/1pdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pdl ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pdl OCA], [http://pdbe.org/1pdl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pdl RCSB], [http://www.ebi.ac.uk/pdbsum/1pdl PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VG05_BPT4 VG05_BPT4]] Tail-associated lysozyme essential for localized hydrolysis of bacterial cell wall necessary for viral DNA injection. The needle-like gp5 protein punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space.
+[https://www.uniprot.org/uniprot/NEEDL_BPT4 NEEDL_BPT4] Tail-associated lysozyme of the baseplate hub that is essential for localized hydrolysis of bacterial cell wall necessary for viral DNA injection. The needle-like gp5 protein punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space. Involved in the tail assembly.<ref>PMID:12837775</ref> <ref>PMID:21129200</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/pd/1pdl_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pd/1pdl_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1pdl ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection.
-Three-dimensional structure of bacteriophage T4 baseplate.,Kostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, van Raaij MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG Nat Struct Biol. 2003 Sep;10(9):688-93. Epub 2003 Aug 17. PMID:12923574<ref>PMID:12923574</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1pdl" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 25: @@
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Bpt4]]
+[[Category: Escherichia virus T4]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Arisaka, F]]
+[[Category: Arisaka F]]
-[[Category: Chipman, P R]]
+[[Category: Chipman PR]]
-[[Category: Kanamaru, S]]
+[[Category: Kanamaru S]]
-[[Category: Kostyuchenko, V A]]
+[[Category: Kostyuchenko VA]]
-[[Category: Leiman, P G]]
+[[Category: Leiman PG]]
-[[Category: Mesyanzhinov, V V]]
+[[Category: Mesyanzhinov VV]]
-[[Category: Raaij, M J.van]]
+[[Category: Rossmann MG]]
-[[Category: Rossmann, M G]]
+[[Category: Van Raaij MJ]]
-[[Category: Hydrolase]]