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1qjy

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Revision as of 07:59, 24 February 2018

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099

Structural highlights

1qjy is a 4 chain structure with sequence from Human rhinovirus 16. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1qju, 1nd3, 1qjx, 1aym, 1ncr, 1nd2, 1ayn, 1c8m, 1tp7, 1xr7, 1d3e
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Rhinoviruses are a frequent cause of the common cold. A series of antirhinoviral compounds have been developed that bind into a hydrophobic pocket in the viral capsid, stabilizing the capsid and interfering with cell attachment. The structures of a variety of such compounds, complexed with rhinovirus serotypes 14, 16, 1A, and 3, previously have been examined. Three chemically similar compounds, closely related to a drug that is undergoing phase III clinical trials, were chosen to determine the structural impact of the heteroatoms in one of the three rings. The compounds were found to have binding modes that depend on their electronic distribution. In the compound with the lowest efficacy, the terminal ring is displaced by 1 A and rotated by 180 degrees relative to the structure of the other two. The greater polarity of the terminal ring in one of the three compounds leads to a small displacement of its position relative to the other compounds in the hydrophobic end of the antiviral compound binding pocket to a site where it makes fewer interactions. Its lower efficacy is likely to be the result of the reduced number of interactions. A region of conserved residues has been identified near the entrance to the binding pocket where there is a corresponding conservation of the mode of binding of these compounds to different serotypes. Thus, variations in residues lining the more hydrophobic end of the pocket are primarily responsible for the differences in drug efficacies.

Analysis of three structurally related antiviral compounds in complex with human rhinovirus 16.,Hadfield AT, Diana GD, Rossmann MG Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):14730-5. PMID:10611281^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hadfield AT, Diana GD, Rossmann MG. Analysis of three structurally related antiviral compounds in complex with human rhinovirus 16. Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):14730-5. PMID:10611281

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qjy"

@@ Line 1: / Line 1: @@
 ==HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099==
 <StructureSection load='1qjy' size='340' side='right' caption='[[1qjy]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qjy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-16 Hrv-16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QJY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QJY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qjy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_16 Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QJY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QJY FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=W03:2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2-METHYL-4-ISOXAZOLYL]-PHENOL'>W03</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">[[1qju|1qju]], [[1nd3|1nd3]], [[1qjx|1qjx]], [[1aym|1aym]], [[1ncr|1ncr]], [[1nd2|1nd2]], [[1ayn|1ayn]], [[1c8m|1c8m]], [[1tp7|1tp7]], [[1xr7|1xr7]], [[1d3e|1d3e]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qjy OCA], [http://pdbe.org/1qjy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qjy RCSB], [http://www.ebi.ac.uk/pdbsum/1qjy PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qjy OCA], [http://pdbe.org/1qjy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qjy RCSB], [http://www.ebi.ac.uk/pdbsum/1qjy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qjy ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qj/1qjy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qj/1qjy_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 1qjy" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[RNA-directed RNA polymerase|RNA-directed RNA polymerase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hrv-16]]
+[[Category: Human rhinovirus 16]]
 [[Category: Diana, G D]]
 [[Category: Hadfield, A T]]
@@ Line 43: / Line 41: @@
 [[Category: Capsid protein]]
 [[Category: Covalent protein-rna linkage]]
+[[Category: Cytoplasm]]
 [[Category: Cytoplasmic vesicle]]
 [[Category: Drug]]
 [[Category: Helicase]]
 [[Category: Host-virus interaction]]
-[[Category: Human rhinovirus 16]]
 [[Category: Hydrolase]]
 [[Category: Lipoprotein]]

1qjy

From Proteopedia

Revision as of 07:59, 24 February 2018

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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