1d3e: Difference between revisions

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-{{Seed}}
-[[Image:1d3e.png|left|200px]]
-<!--
+==CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY==
-The line below this paragraph, containing "STRUCTURE_1d3e", creates the "Structure Box" on the page.
+<SX load='1d3e' size='340' side='right' viewer='molstar' caption='[[1d3e]], [[Resolution|resolution]] 28.00&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'>[[1d3e]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_rhinovirus_sp. Human rhinovirus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3E 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">Electron Microscopy, [[Resolution|Resolution]] 28&#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=1d3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3e OCA], [https://pdbe.org/1d3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3e RCSB], [https://www.ebi.ac.uk/pdbsum/1d3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3e ProSAT]</span></td></tr>
-{{STRUCTURE_1d3e|  PDB=1d3e  |  SCENE=  }}
+</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).
+== 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/d3/1d3e_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=1d3e ConSurf].
+<div style="clear:both"></div>
-===CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY===
+==See Also==
+*[[Intercellular adhesion molecule|Intercellular adhesion molecule]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-<!--
+__TOC__
-The line below this paragraph, {{ABSTRACT_PUBMED_10562537}}, adds the Publication Abstract to the page
+</SX>
-(as it appears on PubMed at http://www.pubmed.gov), where 10562537 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_10562537}}
-==About this Structure==
-D3E is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_rhinovirus_sp. Human rhinovirus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3E OCA].
-==Reference==
-<ref group="xtra">PMID:10562537</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Human rhinovirus sp.]]
+[[Category: Human rhinovirus sp]]
-[[Category: Bella, J.]]
+[[Category: Large Structures]]
-[[Category: Rossmann, M G.]]
+[[Category: Bella J]]
-[[Category: Common cold]]
+[[Category: Rossmann MG]]
-[[Category: Cryo-electron microscopy]]
-[[Category: Fitting of x-ray structures into cryo-em reconstruction]]
-[[Category: Hrv16]]
-[[Category: Human rhinovirus]]
-[[Category: Icam-1]]
-[[Category: Icosahedral virus]]
-[[Category: Rhinovirus-receptor complex]]
-[[Category: Virus uncoating]]
-[[Category: Virus/ viral protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:39:27 2009''