1rud

From Proteopedia

(Difference between revisions)

Current revision

RHINOVIRUS 14 MUTANT N1105S COMPLEXED WITH ANTIVIRAL COMPOUND WIN 52084

Structural highlights

1rud is a 4 chain structure with sequence from Rhinovirus B14. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

Publication Abstract from PubMed

Structures have been determined of three human rhinovirus 14 (HRV14) compensation mutants that have resistance to the antiviral capsid binding compounds WIN 52035 and WIN 52084. In addition, the structure of HRV14 is reported, with a site-directed mutation at residue 1219 in VP1. A spontaneous mutation occurs at the same site in one of the compensation mutants. Some of the mutations are on the viral surface in the canyon and some lie within the hydrophobic binding pocket in VP1 below the ICAM footprint. Those mutant virus strains with mutations on the surface bind better to cells than does wild-type virus. The antiviral compounds bind to the mutant viruses in a manner similar to their binding to wild-type virus. The receptor and WIN compound binding sites overlap, causing competition between receptor attachment and antiviral compound binding. The compensation mutants probably function by shifting the equilibrium in favor of receptor binding. The mutations in the canyon increase the affinity of the virus for the receptor, while the mutations in the pocket probably decrease the affinity of the WIN compounds for the virus by reducing favorable hydrophobic contacts and constricting the pore through which the antiviral compounds are thought to enter the pocket. This is in contrast to the resistant exclusion mutants that block compounds from binding by increasing the bulk of residues within the hydrophobic pocket in VP1.

Structural studies on human rhinovirus 14 drug-resistant compensation mutants.,Hadfield AT, Oliveira MA, Kim KH, Minor I, Kremer MJ, Heinz BA, Shepard D, Pevear DC, Rueckert RR, Rossmann MG J Mol Biol. 1995 Oct 13;253(1):61-73. PMID:7473717^[1]

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

References

↑ Hadfield AT, Oliveira MA, Kim KH, Minor I, Kremer MJ, Heinz BA, Shepard D, Pevear DC, Rueckert RR, Rossmann MG. Structural studies on human rhinovirus 14 drug-resistant compensation mutants. J Mol Biol. 1995 Oct 13;253(1):61-73. PMID:7473717 doi:http://dx.doi.org/10.1006/jmbi.1995.0536

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1rud]] 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=1RUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RUD FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#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=1rud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rud OCA], [https://pdbe.org/1rud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rud RCSB], [https://www.ebi.ac.uk/pdbsum/1rud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rud ProSAT]</span></td></tr>
 </table>

1rud

From Proteopedia

Current revision

RHINOVIRUS 14 MUTANT N1105S COMPLEXED WITH ANTIVIRAL COMPOUND WIN 52084

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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