1ncr

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{{Seed}}
 
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[[Image:1ncr.png|left|200px]]
 
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==The structure of Rhinovirus 16 when complexed with pleconaril, an antiviral compound==
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The line below this paragraph, containing "STRUCTURE_1ncr", creates the "Structure Box" on the page.
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<StructureSection load='1ncr' size='340' side='right'caption='[[1ncr]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ncr]] 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=1NCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NCR FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
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<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=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>
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{{STRUCTURE_1ncr| PDB=1ncr | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ncr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ncr OCA], [https://pdbe.org/1ncr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ncr RCSB], [https://www.ebi.ac.uk/pdbsum/1ncr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ncr ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nc/1ncr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ncr ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===The structure of Rhinovirus 16 when complexed with pleconaril, an antiviral compound===
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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:15452226<ref>PMID:15452226</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1ncr" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15452226}}, adds the Publication Abstract to the page
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*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15452226 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15452226}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1NCR 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=1NCR OCA].
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[[Category: Rhinovirus A16]]
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[[Category: Bator CM]]
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==Reference==
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[[Category: Chakravarty S]]
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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]
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[[Category: Diana G]]
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[[Category: Human rhinovirus 16]]
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[[Category: Pevear DC]]
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[[Category: Protein complex]]
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[[Category: Rossmann MG]]
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[[Category: Bator, C M.]]
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[[Category: Simpson AA]]
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[[Category: Chakravarty, S.]]
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[[Category: Skochko GA]]
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[[Category: Diana, G.]]
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[[Category: Tull TM]]
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[[Category: Pevear, D C.]]
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[[Category: Zhang Y]]
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[[Category: Rossmann, M G.]]
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[[Category: Simpson, A A.]]
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[[Category: Skochko, G A.]]
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[[Category: Tull, T M.]]
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[[Category: Zhang, Y.]]
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[[Category: Hrv16]]
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[[Category: Icosahedral virus]]
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[[Category: Piconavirus]]
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[[Category: Pleconaril]]
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[[Category: Rhinovirus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:11:33 2008''
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Current revision

The structure of Rhinovirus 16 when complexed with pleconaril, an antiviral compound

PDB ID 1ncr

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