1d4m: Difference between revisions
New page: left|200px<br /><applet load="1d4m" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d4m, resolution 2.9Å" /> '''THE CRYSTAL STRUCTURE... |
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== | ==THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION== | ||
BACKGROUND: Coxsackievirus A9 (CAV9), a human pathogen causing symptoms | <StructureSection load='1d4m' size='340' side='right'caption='[[1d4m]], [[Resolution|resolution]] 2.90Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1d4m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_A9 Coxsackievirus A9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D4M FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=W71:5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W71</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=1d4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d4m OCA], [https://pdbe.org/1d4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d4m RCSB], [https://www.ebi.ac.uk/pdbsum/1d4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d4m ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/POLG_CXA9 POLG_CXA9] 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). Capsid proteins interact with host alpha-V/beta-6 integrin heterodimer to provide virion attachment target cell. 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. It also inhibits endoplasmic reticulum-to-Golgi transport (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/d4/1d4m_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1d4m ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Coxsackievirus A9 (CAV9), a human pathogen causing symptoms ranging from common colds to fatal infections of the central nervous system, is an icosahedral single-stranded RNA virus that belongs to the genus Enterovirus of the family Picornaviridae. One of the four capsid proteins, VP1, includes the arginine-glycine-aspartate (RGD) motif within its C-terminal extension. This region binds to integrin alpha v beta 3, the only receptor for CAV9 to be conclusively identified to date. RESULTS: The crystal structure of CAV9 in complex with the antiviral compound WIN 51711 has been solved to 2.9 A resolution. The structures of the four capsid proteins, VP1 to VP4, resemble those of other picornaviruses. The antiviral compound is bound in the VP1 hydrophobic pocket, and it is possible that the pocket entrance contains a second WIN 51711 molecule. Continuous electron density for the VP1 N terminus provides a complete picture of the structure close to the fivefold axis. The VP1 C-terminal portion is on the outer surface of the virus and becomes disordered five-residues N-terminal to the RGD motif. CONCLUSIONS: The RGD motif is exposed and flexible in common with other known integrin ligands. Although CAV9 resembles coxsackie B viruses (CBVs), several substitutions in the areas implicated in CBV receptor attachment suggest it may recognise a different receptor. The structure along the fivefold axis provides new information on the uncoating mechanism of enteroviruses. CAV9 might bind a larger natural pocket factor than other picornaviruses, an observation of particular relevance to the design of new antiviral compounds. | |||
The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses.,Hendry E, Hatanaka H, Fry E, Smyth M, Tate J, Stanway G, Santti J, Maaronen M, Hyypia T, Stuart D Structure. 1999 Dec 15;7(12):1527-38. PMID:10647183<ref>PMID:10647183</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1d4m" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Fry | <references/> | ||
[[Category: Hatanaka | __TOC__ | ||
[[Category: Hendry | </StructureSection> | ||
[[Category: Hyypia | [[Category: Coxsackievirus A9]] | ||
[[Category: Maaronen | [[Category: Large Structures]] | ||
[[Category: Santti | [[Category: Fry E]] | ||
[[Category: Smyth | [[Category: Hatanaka H]] | ||
[[Category: Stanway | [[Category: Hendry E]] | ||
[[Category: Stuart | [[Category: Hyypia T]] | ||
[[Category: Tate | [[Category: Maaronen M]] | ||
[[Category: Santti J]] | |||
[[Category: Smyth M]] | |||
[[Category: Stanway G]] | |||
[[Category: Stuart D]] | |||
[[Category: Tate J]] | |||
