1oke: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1oke.png|left|200px]]
-<!--
+==Crystal structure of the dengue 2 virus envelope protein in complex with n-octyl-beta-D-glucoside==
-The line below this paragraph, containing "STRUCTURE_1oke", creates the "Structure Box" on the page.
+<StructureSection load='1oke' size='340' side='right'caption='[[1oke]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1oke]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus_2 Dengue virus 2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1oam 1oam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OKE FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=1oke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oke OCA], [https://pdbe.org/1oke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oke RCSB], [https://www.ebi.ac.uk/pdbsum/1oke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oke ProSAT]</span></td></tr>
-{{STRUCTURE_1oke|  PDB=1oke  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_DEN2P POLG_DEN2P] Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA (By similarity).  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).  Non-structural protein 2A may be involved viral RNA replication and capsid assembly (Potential).  Non-structural protein 2B is a required cofactor for the serine protease function of NS3 (By similarity).  Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction (By similarity).  Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase (By similarity).  Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter (By similarity).  Non-structural protein 4B inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway (By similarity).  RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway. Inhibits host TYK2 and STAT2 phosphorylation, thereby preventing activation of JAK-STAT signaling pathway (By similarity).
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dengue virus is an emerging global health threat. Its major envelope glycoprotein, E, mediates viral attachment and entry by membrane fusion. A crystal structure of the soluble ectodomain of E from dengue virus type 2 reveals a hydrophobic pocket lined by residues that influence the pH threshold for fusion. The pocket, which accepts a hydrophobic ligand, opens and closes through a conformational shift in a beta-hairpin at the interface between two domains. These features point to a structural pathway for the fusion-activating transition and suggest a strategy for finding small-molecule inhibitors of dengue and other flaviviruses.
-===Crystal structure of the dengue 2 virus envelope protein in complex with n-octyl-beta-D-glucoside===
+A ligand-binding pocket in the dengue virus envelope glycoprotein.,Modis Y, Ogata S, Clements D, Harrison SC Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6986-91. Epub 2003 May 20. PMID:12759475<ref>PMID:12759475</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12759475}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1oke" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12759475 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12759475}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[1oke]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus_2 Dengue virus 2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1oam 1oam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKE OCA].
-==Reference==
-<ref group="xtra">PMID:012759475</ref><ref group="xtra">PMID:007753193</ref><ref group="xtra">PMID:014737159</ref><references group="xtra"/>
 [[Category: Dengue virus 2]]
-[[Category: Harrison, S C.]]
+[[Category: Large Structures]]
-[[Category: Modis, Y.]]
+[[Category: Harrison SC]]
-[[Category: Class 2 fusion protein]]
+[[Category: Modis Y]]
-[[Category: Flavivirus]]
-[[Category: Fusion peptide]]
-[[Category: Low-ph conformational change]]
-[[Category: Membrane fusion]]
-[[Category: Viral protein]]