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| | <StructureSection load='1svp' size='340' side='right'caption='[[1svp]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='1svp' size='340' side='right'caption='[[1svp]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1svp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sindv Sindv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SVP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1svp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sindbis_virus Sindbis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SVP FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SINDBIS VIRUS CAPSID PROTEIN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11034 SINDV])</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]] 2Å</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=1svp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1svp OCA], [https://pdbe.org/1svp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1svp RCSB], [https://www.ebi.ac.uk/pdbsum/1svp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1svp 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=1svp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1svp OCA], [https://pdbe.org/1svp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1svp RCSB], [https://www.ebi.ac.uk/pdbsum/1svp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1svp ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 19: |
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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=1svp 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=1svp ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| - | <div style="background-color:#fffaf0;"> | |
| - | == Publication Abstract from PubMed == | |
| - | BACKGROUND: Many enveloped viruses exit cells by budding from the plasma membrane. The driving force for budding is the interaction of an inner protein nucleocapsid core with transmembrane glycoprotein spikes. The molecular details of this process are ill defined. Alphaviruses, such as Sindbis virus (SINV) and Semliki Forest virus (SFV), represent some of the simplest enveloped viruses and have been well characterized by structural, genetic and biochemical techniques. Although a high-resolution structure of an alphavirus has not yet been attained, cryo-electron microscopy (cryo-EM) has been used to show the multilayer organization at 25 A resolution. In addition, atomic resolution studies are available of the C-terminal domain of the nucleocapsid protein and this has been modeled into the cryo-EM density. RESULTS: A recombinant form of Sindbis virus core protein (SCP) was crystallized and found to diffract much better than protein extracted from the virus (2.0 A versus 3.0 A resolution). The new structure showed that amino acids 108 to 111 bind to a specific hydrophobic pocket in neighboring molecules. Re-examination of the structures derived from virus-extracted protein also showed this 'N-terminal arm' binding to the same hydrophobic pocked in adjacent molecules. It is proposed that the binding of these capsid residues into the hydrophobic pocket of SCP mimics the binding of E2 (one of two glycoproteins that penetrate the lipid bilayer of the viral envelope) C-terminal residues in the pocket. Mutational studies of capsid residues 108 and 110 confirm their role in capsid assembly. CONCLUSIONS: Structural and mutational analyses of residues within the hydrophobic pocket suggest that budding results in a switch between two conformations of the capsid hydrophobic pocket. This is the first description of a viral budding mechanism in molecular detail. | |
| - | | |
| - | Identification of a protein binding site on the surface of the alphavirus nucleocapsid and its implication in virus assembly.,Lee S, Owen KE, Choi HK, Lee H, Lu G, Wengler G, Brown DT, Rossmann MG, Kuhn RJ Structure. 1996 May 15;4(5):531-41. PMID:8736552<ref>PMID:8736552</ref> | |
| - | | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | </div> | |
| - | <div class="pdbe-citations 1svp" style="background-color:#fffaf0;"></div> | |
| | | | |
| | ==See Also== | | ==See Also== |
| Line 36: |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sindv]] | + | [[Category: Sindbis virus]] |
| - | [[Category: Lee, S]] | + | [[Category: Lee S]] |
| - | [[Category: Rossmann, M G]] | + | [[Category: Rossmann MG]] |
| - | [[Category: Chymotrypsin-like serine]]
| + | |
| - | [[Category: Coat protein]]
| + | |
| - | [[Category: Mutant]]
| + | |
| - | [[Category: Sindbis virus capsid protein]]
| + | |
| - | [[Category: Viral protein]]
| + | |
| Structural highlights
Function
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).[1] [2] [3] [4] E3 protein's function is unknown (By similarity).[5] [6] [7] [8] 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).[9] [10] [11] [12] 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.[13] [14] [15] [16] 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).[17] [18] [19] [20]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
See Also
References
- ↑ Smit JM, Bittman R, Wilschut J. Low-pH-dependent fusion of Sindbis virus with receptor-free cholesterol- and sphingolipid-containing liposomes. J Virol. 1999 Oct;73(10):8476-84. PMID:10482600
- ↑ DeTulleo L, Kirchhausen T. The clathrin endocytic pathway in viral infection. EMBO J. 1998 Aug 17;17(16):4585-93. PMID:9707418 doi:10.1093/emboj/17.16.4585
- ↑ Sanz MA, Madan V, Carrasco L, Nieva JL. Interfacial domains in Sindbis virus 6K protein. Detection and functional characterization. J Biol Chem. 2003 Jan 17;278(3):2051-7. Epub 2002 Nov 6. PMID:12424249 doi:10.1074/jbc.M206611200
- ↑ Antoine AF, Montpellier C, Cailliau K, Browaeys-Poly E, Vilain JP, Dubuisson J. The alphavirus 6K protein activates endogenous ionic conductances when expressed in Xenopus oocytes. J Membr Biol. 2007 Jan;215(1):37-48. Epub 2007 May 5. PMID:17483865 doi:10.1007/s00232-007-9003-6
- ↑ Smit JM, Bittman R, Wilschut J. Low-pH-dependent fusion of Sindbis virus with receptor-free cholesterol- and sphingolipid-containing liposomes. J Virol. 1999 Oct;73(10):8476-84. PMID:10482600
- ↑ DeTulleo L, Kirchhausen T. The clathrin endocytic pathway in viral infection. EMBO J. 1998 Aug 17;17(16):4585-93. PMID:9707418 doi:10.1093/emboj/17.16.4585
- ↑ Sanz MA, Madan V, Carrasco L, Nieva JL. Interfacial domains in Sindbis virus 6K protein. Detection and functional characterization. J Biol Chem. 2003 Jan 17;278(3):2051-7. Epub 2002 Nov 6. PMID:12424249 doi:10.1074/jbc.M206611200
- ↑ Antoine AF, Montpellier C, Cailliau K, Browaeys-Poly E, Vilain JP, Dubuisson J. The alphavirus 6K protein activates endogenous ionic conductances when expressed in Xenopus oocytes. J Membr Biol. 2007 Jan;215(1):37-48. Epub 2007 May 5. PMID:17483865 doi:10.1007/s00232-007-9003-6
- ↑ Smit JM, Bittman R, Wilschut J. Low-pH-dependent fusion of Sindbis virus with receptor-free cholesterol- and sphingolipid-containing liposomes. J Virol. 1999 Oct;73(10):8476-84. PMID:10482600
- ↑ DeTulleo L, Kirchhausen T. The clathrin endocytic pathway in viral infection. EMBO J. 1998 Aug 17;17(16):4585-93. PMID:9707418 doi:10.1093/emboj/17.16.4585
- ↑ Sanz MA, Madan V, Carrasco L, Nieva JL. Interfacial domains in Sindbis virus 6K protein. Detection and functional characterization. J Biol Chem. 2003 Jan 17;278(3):2051-7. Epub 2002 Nov 6. PMID:12424249 doi:10.1074/jbc.M206611200
- ↑ Antoine AF, Montpellier C, Cailliau K, Browaeys-Poly E, Vilain JP, Dubuisson J. The alphavirus 6K protein activates endogenous ionic conductances when expressed in Xenopus oocytes. J Membr Biol. 2007 Jan;215(1):37-48. Epub 2007 May 5. PMID:17483865 doi:10.1007/s00232-007-9003-6
- ↑ Smit JM, Bittman R, Wilschut J. Low-pH-dependent fusion of Sindbis virus with receptor-free cholesterol- and sphingolipid-containing liposomes. J Virol. 1999 Oct;73(10):8476-84. PMID:10482600
- ↑ DeTulleo L, Kirchhausen T. The clathrin endocytic pathway in viral infection. EMBO J. 1998 Aug 17;17(16):4585-93. PMID:9707418 doi:10.1093/emboj/17.16.4585
- ↑ Sanz MA, Madan V, Carrasco L, Nieva JL. Interfacial domains in Sindbis virus 6K protein. Detection and functional characterization. J Biol Chem. 2003 Jan 17;278(3):2051-7. Epub 2002 Nov 6. PMID:12424249 doi:10.1074/jbc.M206611200
- ↑ Antoine AF, Montpellier C, Cailliau K, Browaeys-Poly E, Vilain JP, Dubuisson J. The alphavirus 6K protein activates endogenous ionic conductances when expressed in Xenopus oocytes. J Membr Biol. 2007 Jan;215(1):37-48. Epub 2007 May 5. PMID:17483865 doi:10.1007/s00232-007-9003-6
- ↑ Smit JM, Bittman R, Wilschut J. Low-pH-dependent fusion of Sindbis virus with receptor-free cholesterol- and sphingolipid-containing liposomes. J Virol. 1999 Oct;73(10):8476-84. PMID:10482600
- ↑ DeTulleo L, Kirchhausen T. The clathrin endocytic pathway in viral infection. EMBO J. 1998 Aug 17;17(16):4585-93. PMID:9707418 doi:10.1093/emboj/17.16.4585
- ↑ Sanz MA, Madan V, Carrasco L, Nieva JL. Interfacial domains in Sindbis virus 6K protein. Detection and functional characterization. J Biol Chem. 2003 Jan 17;278(3):2051-7. Epub 2002 Nov 6. PMID:12424249 doi:10.1074/jbc.M206611200
- ↑ Antoine AF, Montpellier C, Cailliau K, Browaeys-Poly E, Vilain JP, Dubuisson J. The alphavirus 6K protein activates endogenous ionic conductances when expressed in Xenopus oocytes. J Membr Biol. 2007 Jan;215(1):37-48. Epub 2007 May 5. PMID:17483865 doi:10.1007/s00232-007-9003-6
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