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[[Image:1vcp.jpg|left|200px]]


{{Structure
==SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM I)==
|PDB= 1vcp |SIZE=350|CAPTION= <scene name='initialview01'>1vcp</scene>, resolution 3.0&Aring;
<StructureSection load='1vcp' size='340' side='right'caption='[[1vcp]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>
<table><tr><td colspan='2'>[[1vcp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Semliki_Forest_virus Semliki Forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VCP FirstGlance]. <br>
|ACTIVITY=  
</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&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vcp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcp OCA], [https://pdbe.org/1vcp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vcp RCSB], [https://www.ebi.ac.uk/pdbsum/1vcp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcp ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vcp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcp OCA], [http://www.ebi.ac.uk/pdbsum/1vcp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vcp RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/POLS_SFV POLS_SFV] Capsid protein possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>  E3 protein's function is unknown.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>  E2 is responsible for viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>  6K is a constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>  E1 is a class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>
== 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/vc/1vcp_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1vcp ConSurf].
<div style="clear:both"></div>


'''SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM I)'''
==See Also==
 
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 
== References ==
==Overview==
<references/>
Alphaviruses are enveloped, insect-borne viruses, which contains a positive-sense RNA genome. The protein capsid is surrounded by a lipid membrane, which is penetrated by glycoprotein spikes. The structure of the Sindbis virus (SINV) (the type virus) core protein (SCP) was previously determined and found to have a chymotrypsin-like structure. SCP is a serine proteinase which cleaves itself from a polyprotein. Semliki Forest virus (SFV) is among the most distantly related alphaviruses to SINV. Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the polyprotein by leaving the carboxy-terminal tryptophan in the specificity pocket. The structures of two different crystal forms (I and II) of SFV core protein (SFCP) have been determined to 3.0 A and 3.3 A resolution, respectively. The SFCP monomer backbone structure is very similar to that of SCP. The dimeric association between monomers, A and B, found in two different crystal forms of SCP is also present in both crystal forms of SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While monomers A and B make a tail-to-tail dimer contact, monomers B and C make a head-to-head dimer contact. A hydrophobic pocket on the surface of the capsid protein, the proposed site of binding of the E2 glycoprotein, has large conformational differences with respect to SCP and, in contrast to SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in SCP is pointing into the pocket. The conformation of Tyr184, found in SFCP, is consistent with its availability for iodination, as observed in the homologous SINV cores. This suggests, by comparison with SCP, that E2 binding to cores causes major conformational changes, including the burial of Tyr184, which would stabilize the intact virus on budding from an infected cell. The head-to-tail contacts found in the pentameric and hexameric associations within the virion utilize in the same monomer surface regions as found in the crystalline dimer interfaces.
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1VCP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCP OCA].
[[Category: Semliki Forest virus]]
 
[[Category: Choi H-K]]
==Reference==
[[Category: Lu G]]
Structure of Semliki Forest virus core protein., Choi HK, Lu G, Lee S, Wengler G, Rossmann MG, Proteins. 1997 Mar;27(3):345-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9094737 9094737]
[[Category: Rossmann MG]]
[[Category: Semliki forest virus]]
[[Category: Single protein]]
[[Category: Choi, H K.]]
[[Category: Lu, G.]]
[[Category: Rossmann, M G.]]
[[Category: glycoprotein]]
[[Category: nucleocapsid protein]]
[[Category: polyprotein]]
[[Category: transmembrane]]
[[Category: virus coat protein]]
 
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