1kvp: Difference between revisions

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<SX load='1kvp' size='340' side='right' viewer='molstar' caption='[[1kvp]], [[Resolution|resolution]] 27.00&Aring;' scene=''>
<SX load='1kvp' size='340' side='right' viewer='molstar' caption='[[1kvp]], [[Resolution|resolution]] 27.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1kvp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpphx Bpphx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KVP FirstGlance]. <br>
<table><tr><td colspan='2'>[[1kvp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_phiX174 Escherichia virus phiX174]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KVP FirstGlance]. <br>
</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=1kvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kvp OCA], [https://pdbe.org/1kvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kvp RCSB], [https://www.ebi.ac.uk/pdbsum/1kvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kvp ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 27&#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=1kvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kvp OCA], [https://pdbe.org/1kvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kvp RCSB], [https://www.ebi.ac.uk/pdbsum/1kvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kvp ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/F_BPPHX F_BPPHX]] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F.<ref>PMID:11991963</ref>
[https://www.uniprot.org/uniprot/CAPSD_BPPHS CAPSD_BPPHS] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F (PubMed:11991963, PubMed:1370343, PubMed:8158636). Upon virus binding to host cell, one of the spikes dissociates from the capsid and the virus interacts with LPS through the exposed EF loops on the F proteins (PubMed:29229840). After the genome had been ejected, the channel formed by the F proteins at the unique fivefold axis remains open (PubMed:29229840).<ref>PMID:11991963</ref> <ref>PMID:1370343</ref> <ref>PMID:29229840</ref> <ref>PMID:8158636</ref>
== 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=1kvp 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=1kvp ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Spiroplasma virus, SpV4, is a small, non-enveloped virus that infects the helical mollicute Spiroplasma melliferum. SpV4 exhibits several similarities to the Chlamydia phage, Chp1, and the Coliphages alpha 3, phi K, G4 and phi X174. All of these viruses are members of the Microviridae. These viruses have isometric capsids with T = 1 icosahedral symmetry, cause lytic infections and are the only icosahedral phages that contain single-stranded circular DNA genomes. The aim of this comparative study on these phages was to understand the role of their capsid proteins during host receptor recognition. RESULTS: The three-dimensional structure of SpV4 was determined to 27 A resolution from images of frozen-hydrated particles. Cryo-electron microscopy (cryo-EM) revealed 20, approximately 54 A long, 'mushroom-like' protrusions on the surface of the capsid. Each protrusion comprises a trimeric structure that extends radially along the threefold icosahedral axes of the capsid. A 71 amino acid portion of VP1 (the SpV4 capsid protein) was shown, by structural alignment with the atomic structure of the F capsid protein of phi X174, to represent an insertion sequence between the E and F strands of the eight-stranded antiparallel beta-barrel. Secondary structure prediction of this insertion sequence provided the basis for a probable structural motif, consisting of a six-stranded antiparallel beta sheet connected by small turns. Three such motifs form the rigid stable trimeric structures (mushroom-like protrusions) at the threefold axes, with hydrophobic depressions at their distal surface. CONCLUSIONS: Sequence alignment and structural analysis indicate that distinct genera of the Microviridae might have evolved from a common primordial ancestor, with capsid surface variations, such as the SpV4 protrusions, resulting from gene fusion events that have enabled diverse host ranges. The hydrophobic nature of the cavity at the distal surface of the SpV4 protrusions suggests that this region may function as the receptor-recognition site during host infection.
Structural analysis of the Spiroplasma virus, SpV4: implications for evolutionary variation to obtain host diversity among the Microviridae.,Chipman PR, Agbandje-McKenna M, Renaudin J, Baker TS, McKenna R Structure. 1998 Feb 15;6(2):135-45. PMID:9519405<ref>PMID:9519405</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kvp" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</SX>
</SX>
[[Category: Bpphx]]
[[Category: Escherichia virus phiX174]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: McKenna, R]]
[[Category: McKenna R]]
[[Category: Bacteriophage spv4 coat protein]]
[[Category: Chimera]]
[[Category: Icosahedral virus]]
[[Category: Virus]]

Latest revision as of 07:28, 14 February 2024

STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY

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