1xr7: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1xr7.gif|left|200px]]<br /><applet load="1xr7" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1xr7, resolution 2.30&Aring;" />
-'''Crystal structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 16'''<br />
-==Overview==
+==Crystal structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 16==
-Human rhinoviruses (HRV), the predominant members of the Picornaviridae, family of positive-strand RNA viruses, are the major causative agents of, the common cold. Given the lack of effective treatments for rhinoviral, infections, virally encoded proteins have become attractive therapeutic, targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp), denoted 3Dpol, which is responsible for replicating the viral genome and, for synthesizing a protein primer used in the replication. Here the, crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3Dpol, have been determined. The three structures are very similar to one, another, and to the closely related poliovirus (PV) 3Dpol enzyme. Because, the reported PV crystal structure shows significant disorder, HRV 3Dpol, provides the first complete view of a picornaviral RdRp. The folding, topology of HRV 3Dpol also resembles that of RdRps from hepatitis C virus, (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low, sequence homology.
+<StructureSection load='1xr7' size='340' side='right'caption='[[1xr7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1xr7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_A16 Rhinovirus A16]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1te9 1te9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XR7 FirstGlance]. <br>
-XR7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_2 Human rhinovirus 2]. This structure superseeds the now removed PDB entry 1TE9. Active as [http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1XR7 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=1xr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xr7 OCA], [https://pdbe.org/1xr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xr7 RCSB], [https://www.ebi.ac.uk/pdbsum/1xr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xr7 ProSAT]</span></td></tr>
-==Reference==
+</table>
-The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy., Love RA, Maegley KA, Yu X, Ferre RA, Lingardo LK, Diehl W, Parge HE, Dragovich PS, Fuhrman SA, Structure. 2004 Aug;12(8):1533-44. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15296746 15296746]
+== Function ==
-[[Category: Human rhinovirus 2]]
+[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).
-[[Category: RNA-directed RNA polymerase]]
+== Evolutionary Conservation ==
-[[Category: Single protein]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Diehl, W.]]
+Check<jmol>
-[[Category: Dragovich, P.S.]]
+  <jmolCheckbox>
-[[Category: Ferre, R.A.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/1xr7_consurf.spt"</scriptWhenChecked>
-[[Category: Fuhrman, S.A.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: Lingardo, L.K.]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: Love, R.A.]]
+  </jmolCheckbox>
-[[Category: Maegley, K.A.]]
+</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=1xr7 ConSurf].
-[[Category: Parge, H.E.]]
+<div style="clear:both"></div>
-[[Category: Yu, X.]]
+__TOC__
-[[Category: rna-dependent rna polymerase]]
+</StructureSection>
+[[Category: Large Structures]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:16:58 2007''
+[[Category: Rhinovirus A16]]
+[[Category: Diehl W]]
+[[Category: Dragovich PS]]
+[[Category: Ferre RA]]
+[[Category: Fuhrman SA]]
+[[Category: Lingardo LK]]
+[[Category: Love RA]]
+[[Category: Maegley KA]]
+[[Category: Parge HE]]
+[[Category: Yu X]]