3lob: Difference between revisions

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<StructureSection load='3lob' size='340' side='right'caption='[[3lob]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
<StructureSection load='3lob' size='340' side='right'caption='[[3lob]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3lob]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [https://en.wikipedia.org/wiki/Fhv Fhv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LOB FirstGlance]. <br>
<table><tr><td colspan='2'>[[3lob]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Flock_House_virus Flock House virus] and [https://en.wikipedia.org/wiki/Spodoptera_frugiperda Spodoptera frugiperda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LOB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.6&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P:2-DEOXY-N1,N2-PROPANO+GUANOSINE+MONOPHOSPHATE'>P</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P:2-DEOXY-N1,N2-PROPANO+GUANOSINE+MONOPHOSPHATE'>P</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z2q|2z2q]], [[2q23|2q23]], [[2q25|2q25]], [[2q26|2q26]], [[1f8v|1f8v]], [[1nov|1nov]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alpha, Flock House Virus coat protein alpha ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12287 FHV])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nodavirus_endopeptidase Nodavirus endopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.44 3.4.23.44] </span></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=3lob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lob OCA], [https://pdbe.org/3lob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lob RCSB], [https://www.ebi.ac.uk/pdbsum/3lob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lob ProSAT]</span></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=3lob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lob OCA], [https://pdbe.org/3lob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lob RCSB], [https://www.ebi.ac.uk/pdbsum/3lob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lob ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/CAPSD_FHV CAPSD_FHV]] Capsid protein alpha self-assembles to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins trimers. In addition, 240 calcium ions are incorporated per capsid during assembly. The capsid encapsulates the two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid protein alpha generating capsid protein beta and the membrane-active peptide gamma.  Peptide gamma: membrane-permeabilizing peptide produced by virus maturation, thereby creating the infectious virion. After endocytosis into the host cell, peptide gamma is probably exposed in endosomes, where it permeabilizes the endosomal membrane, facilitating translocation of viral capsid or RNA into the cytoplasm (Probable).  
[https://www.uniprot.org/uniprot/CAPSD_FHV CAPSD_FHV] Capsid protein alpha self-assembles to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins trimers. In addition, 240 calcium ions are incorporated per capsid during assembly. The capsid encapsulates the two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid protein alpha generating capsid protein beta and the membrane-active peptide gamma.  Peptide gamma: membrane-permeabilizing peptide produced by virus maturation, thereby creating the infectious virion. After endocytosis into the host cell, peptide gamma is probably exposed in endosomes, where it permeabilizes the endosomal membrane, facilitating translocation of viral capsid or RNA into the cytoplasm (Probable).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=3lob ConSurf].
</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=3lob ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Divalent metal ions are components of numerous icosahedral virus capsids. Flock House virus (FHV), a small RNA virus of the family Nodaviridae, was utilized as an accessible model system with which to address the effects of metal ions on capsid structure and on the biology of virus-host interactions. Mutations at the calcium-binding sites affected FHV capsid stability and drastically reduced virus infectivity, without altering the overall architecture of the capsid. The mutations also altered the conformation of gamma, a membrane-disrupting, virus-encoded peptide usually sequestered inside the capsid, by increasing its exposure under neutral pH conditions. Our data demonstrate that calcium binding is essential for maintaining a pH-based control on gamma exposure and host membrane disruption, and they reveal a novel rationale for the metal ion requirement during virus entry and infectivity. In the light of the phenotypes displayed by a calcium site mutant of FHV, we suggest that this mutant corresponds to an early entry intermediate formed in the endosomal pathway.
Structure and function of a genetically engineered mimic of a nonenveloped virus entry intermediate.,Banerjee M, Speir JA, Kwan MH, Huang R, Aryanpur PP, Bothner B, Johnson JE J Virol. 2010 May;84(9):4737-46. Epub 2010 Feb 17. PMID:20164221<ref>PMID:20164221</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3lob" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Flock house virus protein B2|Flock house virus protein B2]]
*[[Flock house virus protein B2|Flock house virus protein B2]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Fhv]]
[[Category: Flock House virus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Nodavirus endopeptidase]]
[[Category: Spodoptera frugiperda]]
[[Category: Banerjee, M]]
[[Category: Banerjee M]]
[[Category: Huang, R]]
[[Category: Huang R]]
[[Category: Johnson, J E]]
[[Category: Johnson JE]]
[[Category: Speir, J A]]
[[Category: Speir JA]]
[[Category: Aspartyl protease]]
[[Category: Beta-barrel]]
[[Category: Capsid protein]]
[[Category: Flock house virus]]
[[Category: Hydrolase]]
[[Category: Icosahedral virus]]
[[Category: Jellyroll]]
[[Category: Protease]]
[[Category: Rna]]
[[Category: Virion]]
[[Category: Virus]]
Retrieved from "https://proteopedia.org/3lob"