2j7u - Revision history

OCA at 14:37, 13 December 2023

OCA — Wed, 13 Dec 2023 14:37:33 GMT

←Older revision		Revision as of 14:37, 13 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J7U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J7U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j7w\|2j7w]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [https://pdbe.org/2j7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [https://www.ebi.ac.uk/pdbsum/2j7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7u 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=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [https://pdbe.org/2j7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [https://www.ebi.ac.uk/pdbsum/2j7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~Q6DLV0_9FLAV Q6DLV0_9FLAV~~]~~] 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).[~~SAAS~~:~~SAAS000336_004_099774~~]	+	[https://www.uniprot.org/uniprot/POLG_DEN3S POLG_DEN3S] Capsid protein C: Plays a role in virus budding by binding to the cell membrane and gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. During virus entry, may induce genome penetration into the host cytoplasm after hemifusion induced by the surface proteins. Can migrate to the cell nucleus where it modulates host functions. Overcomes the anti-viral effects of host EXOC1 by sequestering and degrading the latter through the proteasome degradation pathway.[UniProtKB:P17763] Capsid protein C: Inhibits RNA silencing by interfering with host Dicer.[UniProtKB:P03314] Peptide pr: Prevents premature fusion activity of envelope proteins in trans-Golgi by binding to envelope protein E at pH6.0. After virion release in extracellular space, gets dissociated from E dimers.[UniProtKB:P17763] Protein prM: Acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is the only viral peptide matured by host furin in the trans-Golgi network probably to avoid catastrophic activation of the viral fusion activity in acidic Golgi compartment prior to virion release. prM-E cleavage is inefficient, and many virions are only partially matured. These uncleaved prM would play a role in immune evasion.[UniProtKB:P17763] Small envelope protein M: May play a role in virus budding. Exerts cytotoxic effects by activating a mitochondrial apoptotic pathway through M ectodomain. May display a viroporin activity.[UniProtKB:P17763] Envelope protein E: Binds to host cell surface receptor and mediates fusion between viral and cellular membranes. Envelope protein is synthesized in the endoplasmic reticulum in the form of heterodimer with protein prM. They play a role in virion budding in the ER, and the newly formed immature particle is covered with 60 spikes composed of heterodimer between precursor prM and envelope protein E. The virion is transported to the Golgi apparatus where the low pH causes dissociation of PrM-E heterodimers and formation of E homodimers. prM-E cleavage is inefficient, and many virions are only partially matured. These uncleaved prM would play a role in immune evasion.[UniProtKB:P17763] Non-structural protein 1: Involved in immune evasion, pathogenesis and viral replication. Once cleaved off the polyprotein, is targeted to three destinations: the viral replication cycle, the plasma membrane and the extracellular compartment. Essential for viral replication. Required for formation of the replication complex and recruitment of other non-structural proteins to the ER-derived membrane structures. Excreted as a hexameric lipoparticle that plays a role against host immune response. Antagonizing the complement function. Binds to the host macrophages and dendritic cells. Inhibits signal transduction originating from Toll-like receptor 3 (TLR3).[UniProtKB:Q9Q6P4] Non-structural protein 1: Disrupts the host endothelial glycocalyx layer of host pulmonary microvascular endothelial cells, inducing degradation of sialic acid and shedding of heparan sulfate proteoglycans. NS1 induces expression of sialidases, heparanase, and activates cathepsin L, which activates heparanase via enzymatic cleavage. These effects are probably linked to the endothelial hyperpermeability observed in severe dengue disease.[UniProtKB:P17763] Non-structural protein 2A: Component of the viral RNA replication complex that functions in virion assembly and antagonizes the host immune response.[UniProtKB:P17763] Serine protease subunit NS2B: Required cofactor for the serine protease function of NS3. May have membrane-destabilizing activity and form viroporins (By similarity).[UniProtKB:P17763][PROSITE-ProRule:PRU00859] 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.[PROSITE-ProRule:PRU00860] Non-structural protein 4A: Regulates the ATPase activity of the NS3 helicase activity. NS4A allows NS3 helicase to conserve energy during unwinding. Plays a role in the inhibition of the host innate immune response. Interacts with host MAVS and thereby prevents the interaction between DDX58 and MAVS. In turn, IFN-beta production is impaired.[UniProtKB:P17763][UniProtKB:Q9Q6P4] Peptide 2k: Functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter.[UniProtKB:P17763] Non-structural protein 4B: Induces the formation of ER-derived membrane vesicles where the viral replication takes place. 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.[UniProtKB:Q9Q6P4] RNA-directed RNA polymerase NS5: Replicates the viral (+) and (-) RNA 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 RNA 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.[UniProtKB:P17763]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 38:
	[[Category: Dengue virus]]		[[Category: Dengue virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Canard, B]]	+	[[Category: Canard B]]
-	[[Category: Chen~~, Y L~~]]	+	[[Category: Chen YL]]
-	[[Category: Egloff~~, M P~~]]	+	[[Category: Egloff MP]]
-	[[Category: Lescar, J]]	+	[[Category: Lescar J]]
-	[[Category: Malet, H]]	+	[[Category: Malet H]]
-	[[Category: Vasudevan~~, S G~~]]	+	[[Category: Vasudevan SG]]
-	[[Category: Xu, T]]	+	[[Category: Xu T]]
-	[[Category: Yap~~, T L]]~~	+	[[Category: Yap TL]]
-	~~[[Category: Flavivirus]]~~	+
-	~~[[Category: High-throughput assay]]~~	+
-	~~[[Category: Nucleoside binding site]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:03, 19 January 2022

OCA — Wed, 19 Jan 2022 08:03:43 GMT

←Older revision		Revision as of 08:03, 19 January 2022
Line 3:		Line 3:
	<StructureSection load='2j7u' size='340' side='right'caption='[[2j7u]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2j7u' size='340' side='right'caption='[[2j7u]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2J7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J7U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j7w\|2j7w]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [~~http~~://pdbe.org/2j7u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2j7u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7u 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=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [https://pdbe.org/2j7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [https://www.ebi.ac.uk/pdbsum/2j7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/Q6DLV0_9FLAV Q6DLV0_9FLAV]] 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).[SAAS:SAAS000336_004_099774]	+	[[https://www.uniprot.org/uniprot/Q6DLV0_9FLAV Q6DLV0_9FLAV]] 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).[SAAS:SAAS000336_004_099774]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:43, 15 April 2020

OCA — Wed, 15 Apr 2020 07:43:03 GMT

←Older revision		Revision as of 07:43, 15 April 2020
Line 1:		Line 1:

	==Dengue virus NS5 RNA dependent RNA polymerase domain==		==Dengue virus NS5 RNA dependent RNA polymerase domain==
-	<StructureSection load='2j7u' size='340' side='right' caption='[[2j7u]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='2j7u' size='340' side='right'caption='[[2j7u]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2J7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2J7U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://pdbe.org/2j7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7u ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://pdbe.org/2j7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Dengue virus]]		[[Category: Dengue virus]]
		+	[[Category: Large Structures]]
	[[Category: Canard, B]]		[[Category: Canard, B]]
	[[Category: Chen, Y L]]		[[Category: Chen, Y L]]

OCA at 06:42, 11 July 2018

OCA — Wed, 11 Jul 2018 06:42:38 GMT

←Older revision		Revision as of 06:42, 11 July 2018
Line 1:		Line 1:
-	==~~DENGUE VIRUS~~ NS5 RNA ~~DEPENDENT~~ RNA ~~POLYMERASE DOMAIN~~==	+
		+	==Dengue virus NS5 RNA dependent RNA polymerase domain==
	<StructureSection load='2j7u' size='340' side='right' caption='[[2j7u]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2j7u' size='340' side='right' caption='[[2j7u]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://pdbe.org/2j7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://pdbe.org/2j7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j7/2j7u_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j7/2j7u_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 06:08, 10 February 2016

OCA — Wed, 10 Feb 2016 06:08:13 GMT

←Older revision		Revision as of 06:08, 10 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ 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=2j7u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:07, 11 September 2015

OCA — Fri, 11 Sep 2015 06:07:16 GMT

←Older revision		Revision as of 06:07, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://pdbe.org/2j7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q6DLV0_9FLAV Q6DLV0_9FLAV]] 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).[SAAS:SAAS000336_004_099774]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2j7u" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 16:33, 19 January 2015

OCA — Mon, 19 Jan 2015 16:33:22 GMT

←Older revision		Revision as of 16:33, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J7U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J7U FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Dengue virus]]		[[Category: Dengue virus]]
-	[[Category: Canard, B.]]	+	[[Category: Canard, B]]
-	[[Category: Chen, Y L.]]	+	[[Category: Chen, Y L]]
-	[[Category: Egloff, M P.]]	+	[[Category: Egloff, M P]]
-	[[Category: Lescar, J.]]	+	[[Category: Lescar, J]]
-	[[Category: Malet, H.]]	+	[[Category: Malet, H]]
-	[[Category: Vasudevan, S G.]]	+	[[Category: Vasudevan, S G]]
-	[[Category: Xu, T.]]	+	[[Category: Xu, T]]
-	[[Category: Yap, T L.]]	+	[[Category: Yap, T L]]
	[[Category: Flavivirus]]		[[Category: Flavivirus]]
	[[Category: High-throughput assay]]		[[Category: High-throughput assay]]
	[[Category: Nucleoside binding site]]		[[Category: Nucleoside binding site]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

OCA at 03:27, 29 September 2014

OCA — Mon, 29 Sep 2014 03:27:14 GMT

←Older revision		Revision as of 03:27, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2j7u.~~png~~\|~~left~~\|200px]]	+	==DENGUE VIRUS NS5 RNA DEPENDENT RNA POLYMERASE DOMAIN==
		+	<StructureSection load='2j7u' size='340' side='right' caption='[[2j7u]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2j7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J7U FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j7w\|2j7w]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2j7u RCSB], [http://www.ebi.ac.uk/pdbsum/2j7u PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j7/2j7u_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dengue fever, a neglected emerging disease for which no vaccine or antiviral agents exist at present, is caused by dengue virus, a member of the Flavivirus genus, which includes several important human pathogens, such as yellow fever and West Nile viruses. The NS5 protein from dengue virus is bifunctional and contains 900 amino acids. The S-adenosyl methionine transferase activity resides within its N-terminal domain, and residues 270 to 900 form the RNA-dependent RNA polymerase (RdRp) catalytic domain. Viral replication begins with the synthesis of minus-strand RNA from the dengue virus positive-strand RNA genome, which is subsequently used as a template for synthesizing additional plus-strand RNA genomes. This essential function for the production of new viral particles is catalyzed by the NS5 RdRp. Here we present a high-throughput in vitro assay partly recapitulating this activity and the crystallographic structure of an enzymatically active fragment of the dengue virus RdRp refined at 1.85-A resolution. The NS5 nuclear localization sequences, previously thought to fold into a separate domain, form an integral part of the polymerase subdomains. The structure also reveals the presence of two zinc ion binding motifs. In the absence of a template strand, a chain-terminating nucleoside analogue binds to the priming loop site. These results should inform and accelerate the structure-based design of antiviral compounds against dengue virus.

-	~~{{STRUCTURE_2j7u\| PDB=2j7u \| SCENE= }}~~	+	Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution.,Yap TL, Xu T, Chen YL, Malet H, Egloff MP, Canard B, Vasudevan SG, Lescar J J Virol. 2007 May;81(9):4753-65. Epub 2007 Feb 14. PMID:17301146<ref>PMID:17301146</ref>

-	~~===DENGUE VIRUS NS5 RNA DEPENDENT RNA POLYMERASE DOMAIN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17301146}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2j7u]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Dengue_virus Dengue virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017301146<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dengue virus]]		[[Category: Dengue virus]]
	[[Category: Canard, B.]]		[[Category: Canard, B.]]

OCA at 16:35, 20 October 2012

OCA — Sat, 20 Oct 2012 16:35:56 GMT

←Older revision		Revision as of 16:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2j7u]] is a 1 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA].	+	[[2j7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus Dengue virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7U OCA].

	==See Also==		==See Also==

OCA: Protected "2j7u" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 22:11:22 GMT

Protected "2j7u" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:11, 26 July 2012