2plv: Difference between revisions

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-{{Seed}}
-[[Image:2plv.png|left|200px]]
-<!--
+==STRUCTURAL FACTORS THAT CONTROL CONFORMATIONAL TRANSITIONS AND SEROTYPE SPECIFICITY IN TYPE 3 POLIOVIRUS==
-The line below this paragraph, containing "STRUCTURE_2plv", creates the "Structure Box" on the page.
+<StructureSection load='2plv' size='340' side='right'caption='[[2plv]], [[Resolution|resolution]] 2.88&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'>[[2plv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_poliovirus_1_Mahoney Human poliovirus 1 Mahoney]. The August 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Poliovirus and Rhinovirus''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_8 10.2210/rcsb_pdb/mom_2001_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PLV 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]] 2.88&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>
-{{STRUCTURE_2plv|  PDB=2plv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2plv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plv OCA], [https://pdbe.org/2plv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2plv RCSB], [https://www.ebi.ac.uk/pdbsum/2plv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2plv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_POL1M POLG_POL1M] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>   VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>   Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>   Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>   Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>   Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>   Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>   RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</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/pl/2plv_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=2plv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of the Sabin strain of type 3 poliovirus has been determined at 2.4 A resolution. Significant structural differences with the Mahoney strain of type 1 poliovirus are confined to loops and terminal extensions of the capsid proteins, occur in all of the major antigenic sites of the virion and typically involve insertions, deletions or the replacement of prolines. Several newly identified components of the structure participate in assembly-dependent interactions which are relevant to the biologically important processes of viral assembly and uncoating. These include two sites of lipid substitution, two putative nucleotides and a beta sheet formed by the N-termini of capsid proteins VP4 and VP1. The structure provides an explanation for the temperature sensitive phenotype of the P3/Sabin strain. Amino acids that regulate temperature sensitivity in type 3 poliovirus are located in the interfaces between promoters, in the binding site for a lipid substituent and in an assembly-dependent extended beta sheet that stabilizes the association of pentamers. Several lines of evidence indicate that these structural components also control conformational transitions at various stages of the viral life cycle.
-===STRUCTURAL FACTORS THAT CONTROL CONFORMATIONAL TRANSITIONS AND SEROTYPE SPECIFICITY IN TYPE 3 POLIOVIRUS===
+Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus.,Filman DJ, Syed R, Chow M, Macadam AJ, Minor PD, Hogle JM EMBO J. 1989 May;8(5):1567-79. PMID:2548847<ref>PMID:2548847</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2plv" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_2548847}}, adds the Publication Abstract to the page
+*[[Art:Polio: A resolution to eradicate|Art:Polio: A resolution to eradicate]]
-(as it appears on PubMed at http://www.pubmed.gov), where 2548847 is the PubMed ID number.
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_2548847}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-PLV is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Human_poliovirus_1 Human poliovirus 1]. Additional information on 2PLV is available in a page on [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb20_1.html Poliovirus and Rhinovirus] at the RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLV OCA].
+[[Category: Human poliovirus 1 Mahoney]]
+[[Category: Large Structures]]
-==Reference==
-Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus., Filman DJ, Syed R, Chow M, Macadam AJ, Minor PD, Hogle JM, EMBO J. 1989 May;8(5):1567-79. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2548847 2548847]
-[[Category: Human poliovirus 1]]
 [[Category: Poliovirus and Rhinovirus]]
-[[Category: Protein complex]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Filman, D J.]]
+[[Category: Filman DJ]]
-[[Category: Hogle, J M.]]
+[[Category: Hogle JM]]
-[[Category: Icosahedral virus]]
-[[Category: Picornavirus]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 11:11:00 2008''