2rmu: Difference between revisions

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-{{Seed}}
-[[Image:2rmu.png|left|200px]]
-<!--
+==THREE-DIMENSIONAL STRUCTURES OF DRUG-RESISTANT MUTANTS OF HUMAN RHINOVIRUS 14==
-The line below this paragraph, containing "STRUCTURE_2rmu", creates the "Structure Box" on the page.
+<StructureSection load='2rmu' size='340' side='right'caption='[[2rmu]], [[Resolution|resolution]] 3.00&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'>[[2rmu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RMU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RMU 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]] 3&#8491;</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=2rmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rmu OCA], [https://pdbe.org/2rmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rmu RCSB], [https://www.ebi.ac.uk/pdbsum/2rmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rmu ProSAT]</span></td></tr>
-{{STRUCTURE_2rmu|  PDB=2rmu  |  SCENE=  }}
+</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/rm/2rmu_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=2rmu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mutants of human rhinovirus 14 were isolated and characterized by searching for resistance to compounds that inhibit viral uncoating. The portions of the RNA that code for amino acids that surround the antiviral compound binding site were sequenced. X-ray analysis of two of these mutants, 1188 Val----Leu and 1199 Cys----Tyr, shows that these were single-site substitutions which would sterically hinder drug binding. Differences in the resistance of mutant viruses to various antiviral compounds may be rationalized in terms of the three-dimensional structures of these mutants. Predictions of the structures of mutant rhinovirus 14 with the substitutions 1188 Val----Leu, 1199 Cys----Tyr and 1199 Cys----Trp in VP1 were made using a molecular dynamics technique. The predicted structure of the 1199 Cys----Tyr mutant was consistent with the electron density map, while the 1188 Val----Leu prediction was not. Large (up to 1.4 A) conformational differences between native rhinovirus 14 and the 1199 Cys----Tyr mutant occurred in main-chain atoms near the mutation site. These changes, as well as the orientation of the 1199 tyrosine side-chain, were correctly predicted by the molecular dynamics calculation. The structure of the predicted 1199 Cys----Trp mutation is consistent with the drug-resistant properties of this virus.
-===THREE-DIMENSIONAL STRUCTURES OF DRUG-RESISTANT MUTANTS OF HUMAN RHINOVIRUS 14===
+Three-dimensional structures of drug-resistant mutants of human rhinovirus 14.,Badger J, Krishnaswamy S, Kremer MJ, Oliveira MA, Rossmann MG, Heinz BA, Rueckert RR, Dutko FJ, McKinlay MA J Mol Biol. 1989 May 5;207(1):163-74. PMID:2544734<ref>PMID:2544734</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2rmu" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_2544734}}, adds the Publication Abstract to the page
+*[[Human rhinovirus|Human rhinovirus]]
-(as it appears on PubMed at http://www.pubmed.gov), where 2544734 is the PubMed ID number.
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_2544734}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-RMU is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Human_rhinovirus_14 Human rhinovirus 14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RMU OCA].
+[[Category: Large Structures]]
+[[Category: Rhinovirus B14]]
-==Reference==
+[[Category: Badger J]]
-<ref group="xtra">PMID:2544734</ref><references group="xtra"/>
+[[Category: Dutko FJ]]
-[[Category: Human rhinovirus 14]]
+[[Category: Heinz BA]]
-[[Category: Badger, J.]]
+[[Category: Kremer MJ]]
-[[Category: Dutko, F J.]]
+[[Category: Krishnaswamy S]]
-[[Category: Heinz, B A.]]
+[[Category: Mckinlay MA]]
-[[Category: Kremer, M J.]]
+[[Category: Oliveira MA]]
-[[Category: Krishnaswamy, S.]]
+[[Category: Rossmann MG]]
-[[Category: Mckinlay, M A.]]
+[[Category: Rueckert RR]]
-[[Category: Oliveira, M A.]]
-[[Category: Rossmann, M G.]]
-[[Category: Rueckert, R R.]]
-[[Category: Icosahedral virus]]
-[[Category: Rhinovirus coat protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:07:59 2009''