1nd3: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1nd3.jpg|left|200px]]
-<!--
+==The structure of HRV16, when complexed with pleconaril, an antiviral compound==
-The line below this paragraph, containing "STRUCTURE_1nd3", creates the "Structure Box" on the page.
+<StructureSection load='1nd3' size='340' side='right'caption='[[1nd3]], [[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'>[[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>
-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=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>
-{{STRUCTURE_1nd3|  PDB=1nd3  |  SCENE=  }}
+<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>
+</table>
-'''The structure of HRV16, when complexed with pleconaril, an antiviral compound'''
+== Function ==
+[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).
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of human rhinovirus 16 (HRV16) and HRV14 are incubated with pleconaril, drug occupancy in the binding pocket is lower than when pleconaril is introduced during assembly prior to crystallization. This effect is far more marked in HRV16 than in HRV14 and is more marked with pleconaril than with other compounds. These observations are consistent with virus yield inhibition studies and radiolabeled drug binding studies showing that the antiviral effect of pleconaril against HRV16 is greater on the infectivity of progeny virions than the parent input viruses. These data suggest that drug integration into the binding pocket during assembly, or at some other late stage in virus replication, may contribute to the antiviral activity of capsid binding compounds.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1nd3_consurf.spt"</scriptWhenChecked>
-ND3 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Human_rhinovirus_16 Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds., Zhang Y, Simpson AA, Ledford RM, Bator CM, Chakravarty S, Skochko GA, Demenczuk TM, Watanyar A, Pevear DC, Rossmann MG, J Virol. 2004 Oct;78(20):11061-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15452226 15452226]
+</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: Human rhinovirus 16]]
+<div style="clear:both"></div>
-[[Category: Protein complex]]
+__TOC__
-[[Category: Bator, C M.]]
+</StructureSection>
-[[Category: Chakravarty, S.]]
+[[Category: Large Structures]]
-[[Category: Diana, G.]]
+[[Category: Rhinovirus A16]]
-[[Category: Pevear, D C.]]
+[[Category: Bator CM]]
-[[Category: Rossmann, M G.]]
+[[Category: Chakravarty S]]
-[[Category: Simpson, A A.]]
+[[Category: Diana G]]
-[[Category: Skochko, G A.]]
+[[Category: Pevear DC]]
-[[Category: Tull, T M.]]
+[[Category: Rossmann MG]]
-[[Category: Zhang, Y.]]
+[[Category: Simpson AA]]
-[[Category: Hrv16]]
+[[Category: Skochko GA]]
-[[Category: Icosahedral virus]]
+[[Category: Tull TM]]
-[[Category: Piconaviridae]]
+[[Category: Zhang Y]]
-[[Category: Pleconaril]]
-[[Category: Rhinovirus]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:23:17 2008''