3c6r: Difference between revisions

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 <SX load='3c6r' size='340' side='right' viewer='molstar' caption='[[3c6r]], [[Resolution|resolution]] 25.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3c6r]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus_type_2 Dengue virus type 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C6R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3c6r]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus_2_Thailand/PUO-218/1980 Dengue virus 2 Thailand/PUO-218/1980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C6R 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=3c6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c6r OCA], [https://pdbe.org/3c6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c6r RCSB], [https://www.ebi.ac.uk/pdbsum/3c6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c6r 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]] 25&#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=3c6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c6r OCA], [https://pdbe.org/3c6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c6r RCSB], [https://www.ebi.ac.uk/pdbsum/3c6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c6r ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/POLG_DEN2U POLG_DEN2U]] prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity).  Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).  Non-structural protein 1 is involved in virus replication and regulation of the innate immune response. Soluble and membrane-associated NS1 may activate human complement and induce host vascular leakage. This effect might explain the clinical manifestations of dengue hemorrhagic fever and dengue shock syndrome (By similarity).
+[https://www.uniprot.org/uniprot/POLG_DEN2U POLG_DEN2U] prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity).  Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).  Non-structural protein 1 is involved in virus replication and regulation of the innate immune response. Soluble and membrane-associated NS1 may activate human complement and induce host vascular leakage. This effect might explain the clinical manifestations of dengue hemorrhagic fever and dengue shock syndrome (By similarity).
 == Evolutionary Conservation ==
 [[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=3c6r ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Intracellular cleavage of immature flaviviruses is a critical step in assembly that generates the membrane fusion potential of the E glycoprotein. With cryo-electron microscopy we show that the immature dengue particles undergo a reversible conformational change at low pH that renders them accessible to furin cleavage. At a pH of 6.0, the E proteins are arranged in a herringbone pattern with the pr peptides docked onto the fusion loops, a configuration similar to that of the mature virion. After cleavage, the dissociation of pr is pH-dependent, suggesting that in the acidic environment of the trans-Golgi network pr is retained on the virion to prevent membrane fusion. These results suggest a mechanism by which flaviviruses are processed and stabilized in the host cell secretory pathway.
-Structure of the immature dengue virus at low pH primes proteolytic maturation.,Yu IM, Zhang W, Holdaway HA, Li L, Kostyuchenko VA, Chipman PR, Kuhn RJ, Rossmann MG, Chen J Science. 2008 Mar 28;319(5871):1834-7. PMID:18369148<ref>PMID:18369148</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3c6r" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </SX>
-[[Category: Dengue virus type 2]]
+[[Category: Dengue virus 2 Thailand/PUO-218/1980]]
 [[Category: Large Structures]]
-[[Category: Chen, J]]
+[[Category: Chen J]]
-[[Category: Chipman, P R]]
+[[Category: Chipman PR]]
-[[Category: Holdway, H A]]
+[[Category: Holdway HA]]
-[[Category: Kostyuchenko, V A]]
+[[Category: Kostyuchenko VA]]
-[[Category: Kuhn, R J]]
+[[Category: Kuhn RJ]]
-[[Category: Li, L]]
+[[Category: Li L]]
-[[Category: Rossmann, M G]]
+[[Category: Rossmann MG]]
-[[Category: Yu, I]]
+[[Category: Yu I]]
-[[Category: Zhang, W]]
+[[Category: Zhang W]]
-[[Category: Capsid protein]]
-[[Category: Cleavage on pair of basic residue]]
-[[Category: Core protein]]
-[[Category: Dengue]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Envelope protein]]
-[[Category: Glycoprotein]]
-[[Category: Icosahedral virus]]
-[[Category: Immature]]
-[[Category: Membrane]]
-[[Category: Prm]]
-[[Category: Secreted]]
-[[Category: Transmembrane]]
-[[Category: Virion]]
-[[Category: Virus]]