1c8m
From Proteopedia
(Difference between revisions)
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<StructureSection load='1c8m' size='340' side='right'caption='[[1c8m]], [[Resolution|resolution]] 2.80Å' scene=''> | <StructureSection load='1c8m' size='340' side='right'caption='[[1c8m]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1c8m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1c8m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_A16 Rhinovirus A16]. The August 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Poliovirus and Rhinovirus'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_8 10.2210/rcsb_pdb/mom_2001_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C8M FirstGlance]. <br> |
</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> | </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> | ||
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ayn|1ayn]], [[1aym|1aym]], [[1qju|1qju]], [[1qjx|1qjx]], [[1qjy|1qjy]]</div></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=1c8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c8m OCA], [https://pdbe.org/1c8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c8m RCSB], [https://www.ebi.ac.uk/pdbsum/1c8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c8m ProSAT]</span></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=1c8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c8m OCA], [https://pdbe.org/1c8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c8m RCSB], [https://www.ebi.ac.uk/pdbsum/1c8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c8m ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Human rhinovirus 16]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Poliovirus and Rhinovirus]] | [[Category: Poliovirus and Rhinovirus]] | ||
[[Category: RCSB PDB Molecule of the Month]] | [[Category: RCSB PDB Molecule of the Month]] | ||
| - | [[Category: | + | [[Category: Rhinovirus A16]] |
| - | [[Category: | + | [[Category: Bator CM]] |
| - | [[Category: | + | [[Category: Chakravarty S]] |
| - | [[Category: | + | [[Category: Diana GD]] |
| - | [[Category: | + | [[Category: Pevear DC]] |
| - | [[Category: | + | [[Category: Rossmann MG]] |
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Revision as of 06:50, 8 February 2023
REFINED CRYSTAL STRUCTURE OF HUMAN RHINOVIRUS 16 COMPLEXED WITH VP63843 (PLECONARIL), AN ANTI-PICORNAVIRAL DRUG CURRENTLY IN CLINICAL TRIALS
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