1nd2: Difference between revisions

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 <StructureSection load='1nd2' size='340' side='right'caption='[[1nd2]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nd2]] is a 4 chain structure with sequence from [https://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=1ND2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nd2]] 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=1ND2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND2 FirstGlance]. <br>
-</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=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ncr|1ncr]], [[1ncq|1ncq]], [[1na1|1na1]]</div></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=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd2 OCA], [https://pdbe.org/1nd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nd2 RCSB], [https://www.ebi.ac.uk/pdbsum/1nd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd2 ProSAT]</span></td></tr>
 </table>
 == 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).
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=1nd2 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1nd2" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Human rhinovirus 16]]
 [[Category: Large Structures]]
-[[Category: Bator, C M]]
+[[Category: Rhinovirus A16]]
-[[Category: Chakravarty, S]]
+[[Category: Bator CM]]
-[[Category: Diana, G]]
+[[Category: Chakravarty S]]
-[[Category: Pevear, D C]]
+[[Category: Diana G]]
-[[Category: Rossmann, M G]]
+[[Category: Pevear DC]]
-[[Category: Simpson, A A]]
+[[Category: Rossmann MG]]
-[[Category: Skochko, G A]]
+[[Category: Simpson AA]]
-[[Category: Tull, T M]]
+[[Category: Skochko GA]]
-[[Category: Zhang, Y]]
+[[Category: Tull TM]]
-[[Category: Hrv 16]]
+[[Category: Zhang Y]]
-[[Category: Icosahedral virus]]
-[[Category: Piconaviridae]]
-[[Category: Pocket factor]]
-[[Category: Rhinovirus]]
-[[Category: Virus]]