2snw: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[2snw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sindbis_virus Sindbis virus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1snw 1snw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2SNW 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=2snw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2snw OCA], [https://pdbe.org/2snw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2snw RCSB], [https://www.ebi.ac.uk/pdbsum/2snw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2snw ProSAT]</span></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]] 2.7&#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=2snw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2snw OCA], [https://pdbe.org/2snw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2snw RCSB], [https://www.ebi.ac.uk/pdbsum/2snw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2snw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/POLS_SINDV POLS_SINDV]] 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 (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</ref>   E3 protein's function is unknown (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</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 (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</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:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</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 (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</ref>
+[https://www.uniprot.org/uniprot/POLS_SINDV POLS_SINDV] 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 (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</ref>   E3 protein's function is unknown (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</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 (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</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:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</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 (By similarity).<ref>PMID:10482600</ref> <ref>PMID:9707418</ref> <ref>PMID:12424249</ref> <ref>PMID:17483865</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 19: @@
 </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=2snw ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Sindbis virus core protein (SCP) has been isolated from virus and crystallized. The X-ray crystallographic structure showed that the amino-terminal 113 residues appeared to be either disordered or truncated during crystallization and that the carboxy-terminal residues 114 to 264 had a chymotrypsin-like structure. The carboxy-terminal residues 106 to 264 and 106 to 266 of SCP have now been expressed in Escherichia coli. Most crystal forms of the truncated proteins were isomorphous with those of the virally extracted protein. There are only small structural differences between the truncated recombinant protein and the ordered part of the wild-type virus-extracted protein. Hence, E. coli-expressed SCP can be used to study proteolytic properties and the contribution of SCP to nucleocapsid assembly, interaction with the E2 glycoprotein and interaction with RNA. The same dimer that was found in two different crystal forms of the virus-extracted SCP was present also in some of the crystals of the truncated recombinant protein. The monomer-monomer interface is maintained by two pairs of hydrogen bonds and by hydrophobic interactions. Removal of the hydrogen bonds by single substitutions did not prevent dimer formation. However, a mutation that reduced the hydrophobic contacts did inhibit dimer formation. The wild-type truncated SCP is active in E. coli, as evidenced by proteolytic processing of a series of progressively longer precursors that extend beyond residue 264. Unlike the virus-extracted capsid protein, the E. coli-expressed SCP described here is terminated following the carboxy-terminal residue and, therefore, does not require autocatalysis. Nevertheless, the E. coli-expressed protein folds with the carboxy-terminal tryptophan residue in the specificity pocket. Two crystallographically independent molecules of SCP(106 to 266), which had two additional downstream residues and had the essential S215 mutated to alanine, showed two distinct modes of binding the uncleaved carboxy-terminal residues. These may represent successive steps of binding substrate prior to catalytic cleavage. Refinement of the various crystal structures of SCP showed that the amino-terminal arm from residues 107 to 113 was not disordered, but is associated with neighboring molecules. Residues 108 to 111 bind into a hydrophobic pocket composed primarily of Y180, W247 and F166. It had been shown that the double mutant (Y180S; E183G), with the Y180S substitution in this pocket, produced a large number of non-infectious virions, possibly because of modification in the interaction of the glycoprotein spikes with core proteins. The crystal structure of this double mutant showed that there was a large positional change in the side-chain of W247, which moved into the space created by the replacement of Y180 with serine. These conformational changes may alter the stability of the virion and, thus, regulate its functional requirements during cell entry.
-Structural analysis of Sindbis virus capsid mutants involving assembly and catalysis.,Choi HK, Lee S, Zhang YP, McKinney BR, Wengler G, Rossmann MG, Kuhn RJ J Mol Biol. 1996 Sep 20;262(2):151-67. PMID:8831786<ref>PMID:8831786</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2snw" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 36: / Line 28: @@
 [[Category: Large Structures]]
 [[Category: Sindbis virus]]
-[[Category: Choi, H K]]
+[[Category: Choi H-K]]
-[[Category: Kuhn, R J]]
+[[Category: Kuhn RJ]]
-[[Category: Lee, S]]
+[[Category: Lee S]]
-[[Category: Mckinney, B R]]
+[[Category: Mckinney BR]]
-[[Category: Rossmann, M G]]
+[[Category: Rossmann MG]]
-[[Category: Wengler, G]]
+[[Category: Wengler G]]
-[[Category: Zhang, Y P]]
+[[Category: Zhang Y-P]]
-[[Category: Alphavirus]]
-[[Category: Capsid]]
-[[Category: Chymotrypsin]]
-[[Category: Proteinase]]
-[[Category: Sindbi]]
-[[Category: Viral protein]]
-[[Category: Virus]]
-[[Category: Virus coat protein]]