2rs1: Difference between revisions

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-[[Image:2rs1.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2rs1", creates the "Structure Box" on the page.
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-{{STRUCTURE_2rs1|  PDB=2rs1  |  SCENE=  }}
-'''STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES'''
+==STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES==
+<StructureSection load='2rs1' size='340' side='right'caption='[[2rs1]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2rs1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rhinovirus_sp. Human rhinovirus sp.] and [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rs1 1rs1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RS1 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W84:5-(7-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W84</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=2rs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rs1 OCA], [https://pdbe.org/2rs1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rs1 RCSB], [https://www.ebi.ac.uk/pdbsum/2rs1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rs1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_HRV14 POLG_HRV14] 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 (By similarity). 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.  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]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rs/2rs1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2rs1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.
-==Overview==
+Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.,Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG Proteins. 1989;6(1):1-19. PMID:2558377<ref>PMID:2558377</ref>
-X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-RS1 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Human_rhinovirus_14 Human rhinovirus 14] and [http://en.wikipedia.org/wiki/Human_rhinovirus_sp. Human rhinovirus sp.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rs1 1rs1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RS1 OCA].
+</div>
+<div class="pdbe-citations 2rs1" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses., Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG, Proteins. 1989;6(1):1-19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2558377 2558377]
+*[[Human rhinovirus|Human rhinovirus]]
-[[Category: Human rhinovirus 14]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-[[Category: Human rhinovirus sp.]]
+== References ==
-[[Category: Protein complex]]
+<references/>
-[[Category: Badger, J.]]
+__TOC__
-[[Category: Rossmann, M G.]]
+</StructureSection>
-[[Category: Smith, T J.]]
+[[Category: Human rhinovirus sp]]
-[[Category: Icosahedral virus]]
+[[Category: Large Structures]]
-[[Category: Rhinovirus coat protein]]
+[[Category: Rhinovirus B14]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 17:15:03 2008''
+[[Category: Badger J]]
+[[Category: Rossmann MG]]
+[[Category: Smith TJ]]