1xr5: Difference between revisions

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-[[Image:1xr5.gif|left|200px]]
-<!--
+==Crystal Structure of the RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 14==
-The line below this paragraph, containing "STRUCTURE_1xr5", creates the "Structure Box" on the page.
+<StructureSection load='1xr5' size='340' side='right'caption='[[1xr5]], [[Resolution|resolution]] 2.80&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'>[[1xr5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1teb 1teb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XR5 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene></td></tr>
-{{STRUCTURE_1xr5|  PDB=1xr5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xr5 OCA], [https://pdbe.org/1xr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xr5 RCSB], [https://www.ebi.ac.uk/pdbsum/1xr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xr5 ProSAT]</span></td></tr>
+</table>
-'''Crystal Structure of the RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 14'''
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_HRV14 POLG_HRV14] 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 (By similarity). The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis.  VP0 precursor is a component of immature procapsids (By similarity).  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 (By similarity).  Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).  Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).  Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).  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).  RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) denoted 3Dpol, which is responsible for replicating the viral genome and for synthesizing a protein primer used in the replication. Here the crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3Dpol have been determined. The three structures are very similar to one another, and to the closely related poliovirus (PV) 3Dpol enzyme. Because the reported PV crystal structure shows significant disorder, HRV 3Dpol provides the first complete view of a picornaviral RdRp. The folding topology of HRV 3Dpol also resembles that of RdRps from hepatitis C virus (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low sequence homology.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/1xr5_consurf.spt"</scriptWhenChecked>
-XR5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_14 Human rhinovirus 14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1teb 1teb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XR5 OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy., Love RA, Maegley KA, Yu X, Ferre RA, Lingardo LK, Diehl W, Parge HE, Dragovich PS, Fuhrman SA, Structure. 2004 Aug;12(8):1533-44. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15296746 15296746]
+</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=1xr5 ConSurf].
-[[Category: Human rhinovirus 14]]
+<div style="clear:both"></div>
-[[Category: RNA-directed RNA polymerase]]
+__TOC__
-[[Category: Single protein]]
+</StructureSection>
-[[Category: Diehl, W.]]
+[[Category: Large Structures]]
-[[Category: Dragovich, P S.]]
+[[Category: Rhinovirus B14]]
-[[Category: Ferre, R A.]]
+[[Category: Diehl W]]
-[[Category: Fuhrman, S A.]]
+[[Category: Dragovich PS]]
-[[Category: Lingardo, L K.]]
+[[Category: Ferre RA]]
-[[Category: Love, R A.]]
+[[Category: Fuhrman SA]]
-[[Category: Maegley, K A.]]
+[[Category: Lingardo LK]]
-[[Category: Parge, H E.]]
+[[Category: Love RA]]
-[[Category: Yu, X.]]
+[[Category: Maegley KA]]
-[[Category: Rna-dependent rna polymerase]]
+[[Category: Parge HE]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 15:24:04 2008''
+[[Category: Yu X]]