1nd3: Difference between revisions

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-[[Image:1nd3.png|left|200px]]
-{{STRUCTURE_1nd3|  PDB=1nd3  |  SCENE=  }}
+==The structure of HRV16, when complexed with pleconaril, an antiviral compound==
+<StructureSection load='1nd3' size='340' side='right'caption='[[1nd3]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-===The structure of HRV16, when complexed with pleconaril, an antiviral compound===
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_A16 Rhinovirus A16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
-{{ABSTRACT_PUBMED_15452226}}
+</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=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-==About this Structure==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [https://pdbe.org/1nd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd3 ProSAT]</span></td></tr>
-[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA].
+</table>
+== Function ==
-==Reference==
+[https://www.uniprot.org/uniprot/POLG_HRV16 POLG_HRV16] 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 capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis (By similarity).  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).
-<ref group="xtra">PMID:015452226</ref><references group="xtra"/>
+== Evolutionary Conservation ==
-[[Category: Human rhinovirus a16]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Bator, C M.]]
+Check<jmol>
-[[Category: Chakravarty, S.]]
+  <jmolCheckbox>
-[[Category: Diana, G.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1nd3_consurf.spt"</scriptWhenChecked>
-[[Category: Pevear, D C.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: Rossmann, M G.]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: Simpson, A A.]]
+  </jmolCheckbox>
-[[Category: Skochko, G A.]]
+</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=1nd3 ConSurf].
-[[Category: Tull, T M.]]
+<div style="clear:both"></div>
-[[Category: Zhang, Y.]]
+__TOC__
-[[Category: Hrv16]]
+</StructureSection>
-[[Category: Icosahedral virus]]
+[[Category: Large Structures]]
-[[Category: Piconaviridae]]
+[[Category: Rhinovirus A16]]
-[[Category: Pleconaril]]
+[[Category: Bator CM]]
-[[Category: Rhinovirus]]
+[[Category: Chakravarty S]]
-[[Category: Virus]]
+[[Category: Diana G]]
+[[Category: Pevear DC]]
+[[Category: Rossmann MG]]
+[[Category: Simpson AA]]
+[[Category: Skochko GA]]
+[[Category: Tull TM]]
+[[Category: Zhang Y]]