2r5k: Difference between revisions

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 ==Pentamer Structure of Major Capsid protein L1 of Human Papilloma Virus type 11==
-<StructureSection load='2r5k' size='340' side='right' caption='[[2r5k]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='2r5k' size='340' side='right'caption='[[2r5k]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2r5k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_papillomavirus_type_11 Human papillomavirus type 11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R5K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2r5k]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_papillomavirus_11 Human papillomavirus 11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R5K FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2r5h|2r5h]], [[2r5i|2r5i]], [[2r5j|2r5j]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">L1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10580 Human papillomavirus type 11])</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=2r5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r5k OCA], [https://pdbe.org/2r5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r5k RCSB], [https://www.ebi.ac.uk/pdbsum/2r5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r5k 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=2r5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r5k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r5k RCSB], [http://www.ebi.ac.uk/pdbsum/2r5k PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VL1_HPV11 VL1_HPV11]] Forms an icosahedral capsid with a T=7 symmetry and about 55 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. The capsid encapsulates the genomic DNA, but does not bind DNA. Essential for the initial attachment to the host cell (By similarity).
+[https://www.uniprot.org/uniprot/VL1_HPV11 VL1_HPV11] Forms an icosahedral capsid with a T=7 symmetry and about 55 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. The capsid encapsulates the genomic DNA, but does not bind DNA. Essential for the initial attachment to the host cell (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/r5/2r5k_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r5/2r5k_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=2r5k ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Human papillomaviruses (HPVs) are known etiologic agents of cervical cancer. Vaccines that contain virus-like particles (VLPs) made of L1 capsid protein from several high risk HPV types have proven to be effective against HPV infections. Raising high levels of neutralizing antibodies against each HPV type is believed to be the primary mechanism of protection, gained by vaccination. Antibodies elicited by a particular HPV type are highly specific to that particular HPV type and show little or no cross-reactivity between HPV types. With an intention to understand the interplay between the L1 structure of different HPV types and the type specificity of neutralizing antibodies, we have prepared the L1 pentamers of four different HPV types, HPV11, HPV16, HPV18, and HPV35. The pentamers only bind the type-specific neutralizing monoclonal antibodies (NmAbs) that are raised against the VLP of the corresponding HPV type, implying that the surface loop structures of the pentamers from each type are distinctive and functionally active as VLPs in terms of antibody binding. We have determined the crystal structures of all four L1 pentamers, and their comparisons revealed characteristic conformational differences of the surface loops that contain the known epitopes for the NmAbs. On the basis of these distinct surface loop structures, we have provided a molecular explanation for the type specificity of NmAbs against HPV infection.
-Crystal structures of four types of human papillomavirus L1 capsid proteins: understanding the specificity of neutralizing monoclonal antibodies.,Bishop B, Dasgupta J, Klein M, Garcea RL, Christensen ND, Zhao R, Chen XS J Biol Chem. 2007 Oct 26;282(43):31803-11. Epub 2007 Sep 4. PMID:17804402<ref>PMID:17804402</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Virus coat protein|Virus coat protein]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Human papillomavirus type 11]]
+[[Category: Human papillomavirus 11]]
-[[Category: Bishop, B]]
+[[Category: Large Structures]]
-[[Category: Chen, X S]]
+[[Category: Bishop B]]
-[[Category: Dasgupta, J]]
+[[Category: Chen XS]]
-[[Category: Capsid]]
+[[Category: Dasgupta J]]
-[[Category: Capsid protein]]
-[[Category: Hpv11]]
-[[Category: Late protein]]
-[[Category: Pentamer]]
-[[Category: Type specific epitope]]
-[[Category: Viral protein]]
-[[Category: Virion]]