2jv6: Difference between revisions

Line 1:

==YF ED3 Protein NMR Structure==

== Structural highlights ==

<table><tr><td colspan='2'>[[2jv6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Flavivirus_febricis Flavivirus febricis~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JV6 OCA]. For a guided tour on the structure components use [https://proteopedia.org/fgij/fg.htm?mol=2JV6 FirstGlance].

<table><tr><td colspan='2'>[[2jv6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JV6 OCA]. For a guided tour on the structure components use [https://proteopedia.org/fgij/fg.htm?mol=2JV6 FirstGlance].

</td></tr><tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[https://proteopedia.org/fgij/fg.htm?mol=2jv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jv6 OCA], [https://pdbe.org/2jv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jv6 RCSB], [https://www.ebi.ac.uk/pdbsum/2jv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jv6 ProSAT]</td></tr>

</td></tr><tr id='method'><td class="sblockLbl">[[Empirical_models|Method:]]</td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr>

<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[https://proteopedia.org/fgij/fg.htm?mol=2jv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jv6 OCA], [https://pdbe.org/2jv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jv6 RCSB], [https://www.ebi.ac.uk/pdbsum/2jv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jv6 ProSAT]</td></tr>

</table>

~~== Function ==~~

[[https://www.uniprot.org/uniprot/POLG_YEFVC POLG_YEFVC]] 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 (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 (By similarity).

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Line 13:

Line 12:

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jv/2jv6_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>

<text>to colour the structure by Evolutionary Conservation</text>

</jmolCheckbox>

Line 20:

Line 19:

__TOC__

</StructureSection>

~~[[Category: Flavivirus febricis]]~~

[[Category: Large Structures]]

[[Category: ~~Anderson, A~~]]

[[Category: Yellow fever virus]]

[[Category: ~~Barrett,~~ A ~~D.T~~]]

[[Category: Anderson A]]

[[Category: ~~Gandham, S H.A~~]]

[[Category: Barrett ADT]]

[[Category: ~~Gorenstein, D G~~]]

[[Category: Gandham SHA]]

[[Category: ~~May, F J~~]]

[[Category: Gorenstein DG]]

[[Category: ~~Volk, D E~~]]

[[Category: May FJ]]

[[Category: ~~Atp-binding]]~~

[[Category: Volk DE]]

~~[[Category: Capsid protein]]~~

~~[[Category: Cleavage on pair of basic residue]]~~

~~[[Category: Endoplasmic reticulum]]~~

~~[[Category: Envelop protein domain iii]]~~

~~[[Category: Envelope protein]]~~

~~[[Category: Flavivirus]]~~

~~[[Category: Glycoprotein]]~~

~~[[Category: Helicase]]~~

~~[[Category: Hydrolase]]~~

~~[[Category: Membrane]]~~

~~[[Category: Metal-binding]]~~

~~[[Category: Multifunctional enzyme]]~~

~~[[Category: Nucleotide-binding]]~~

~~[[Category: Nucleotidyltransferase]]~~

~~[[Category: Nucleus]]~~

~~[[Category: Phosphorylation]]~~

~~[[Category: Protease]]~~

~~[[Category: Ribonucleoprotein]]~~

~~[[Category: Rna replication]]~~

~~[[Category: Rna-binding]]~~

~~[[Category: Rna-directed rna polymerase]]~~

~~[[Category: Secreted]]~~

~~[[Category: Serine protease]]~~

~~[[Category: Transferase]]~~

~~[[Category: Transmembrane]]~~

~~[[Category: Viral nucleoprotein]]~~

~~[[Category: Viral protein]]~~

~~[[Category: Virion]]~~

~~[[Category: Yellow fever~~]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
 ==YF ED3 Protein NMR Structure==
-<StructureSection load='2jv6' size='340' side='right'caption='[[2jv6]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2jv6' size='340' side='right'caption='[[2jv6]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jv6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavivirus_febricis Flavivirus febricis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JV6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jv6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JV6 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=2jv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jv6 OCA], [https://pdbe.org/2jv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jv6 RCSB], [https://www.ebi.ac.uk/pdbsum/2jv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jv6 ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</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=2jv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jv6 OCA], [https://pdbe.org/2jv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jv6 RCSB], [https://www.ebi.ac.uk/pdbsum/2jv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jv6 ProSAT]</span></td></tr>
 </table>
-== Function ==
-[[https://www.uniprot.org/uniprot/POLG_YEFVC POLG_YEFVC]] 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 (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 (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 12: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jv/2jv6_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 20: / Line 19: @@
 __TOC__
 </StructureSection>
-[[Category: Flavivirus febricis]]
 [[Category: Large Structures]]
-[[Category: Anderson, A]]
+[[Category: Yellow fever virus]]
-[[Category: Barrett, A D.T]]
+[[Category: Anderson A]]
-[[Category: Gandham, S H.A]]
+[[Category: Barrett ADT]]
-[[Category: Gorenstein, D G]]
+[[Category: Gandham SHA]]
-[[Category: May, F J]]
+[[Category: Gorenstein DG]]
-[[Category: Volk, D E]]
+[[Category: May FJ]]
-[[Category: Atp-binding]]
+[[Category: Volk DE]]
-[[Category: Capsid protein]]
-[[Category: Cleavage on pair of basic residue]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Envelop protein domain iii]]
-[[Category: Envelope protein]]
-[[Category: Flavivirus]]
-[[Category: Glycoprotein]]
-[[Category: Helicase]]
-[[Category: Hydrolase]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Multifunctional enzyme]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Nucleus]]
-[[Category: Phosphorylation]]
-[[Category: Protease]]
-[[Category: Ribonucleoprotein]]
-[[Category: Rna replication]]
-[[Category: Rna-binding]]
-[[Category: Rna-directed rna polymerase]]
-[[Category: Secreted]]
-[[Category: Serine protease]]
-[[Category: Transferase]]
-[[Category: Transmembrane]]
-[[Category: Viral nucleoprotein]]
-[[Category: Viral protein]]
-[[Category: Virion]]
-[[Category: Yellow fever]]