7bm0 - Revision history

OCA at 12:30, 1 February 2024

2024-02-01T12:30:43Z

←Older revision		Revision as of 12:30, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7bm0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tick-borne_encephalitis_virus Tick-borne encephalitis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BM0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7bm0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tick-borne_encephalitis_virus Tick-borne encephalitis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BM0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7bm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bm0 OCA], [https://pdbe.org/7bm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bm0 RCSB], [https://www.ebi.ac.uk/pdbsum/7bm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bm0 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=7bm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bm0 OCA], [https://pdbe.org/7bm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bm0 RCSB], [https://www.ebi.ac.uk/pdbsum/7bm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bm0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_TBEVW POLG_TBEVW]] 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). 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 SCRIB and prevents activation of downstream JAK-STAT signaling pathway (By similarity).	+	[https://www.uniprot.org/uniprot/POLG_TBEVW POLG_TBEVW] 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). 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 SCRIB and prevents activation of downstream JAK-STAT signaling pathway (By similarity).
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:46, 7 September 2022

2022-09-07T16:46:23Z

←Older revision		Revision as of 16:46, 7 September 2022
Line 1:		Line 1:

	==Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with AMPPNP==		==Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with AMPPNP==
-	<StructureSection load='7bm0' size='340' side='right'caption='[[7bm0]]' scene=''>	+	<StructureSection load='7bm0' size='340' side='right'caption='[[7bm0]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BM0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bm0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tick-borne_encephalitis_virus Tick-borne encephalitis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BM0 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=7bm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bm0 OCA], [https://pdbe.org/7bm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bm0 RCSB], [https://www.ebi.ac.uk/pdbsum/7bm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bm0 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7bm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bm0 OCA], [https://pdbe.org/7bm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bm0 RCSB], [https://www.ebi.ac.uk/pdbsum/7bm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bm0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/POLG_TBEVW POLG_TBEVW]] 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). 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 SCRIB and prevents activation of downstream JAK-STAT signaling pathway (By similarity).
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Tick-borne encephalitis virus]]
	[[Category: Anindita PD]]		[[Category: Anindita PD]]
	[[Category: Franta Z]]		[[Category: Franta Z]]
	[[Category: Grinkevich P]]		[[Category: Grinkevich P]]

OCA at 06:15, 2 March 2022

2022-03-02T06:15:28Z

←Older revision		Revision as of 06:15, 2 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7bm0 is ON HOLD until Paper Publication~~	+	==Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with AMPPNP==
-		+	<StructureSection load='7bm0' size='340' side='right'caption='[[7bm0]]' scene=''>
-	~~Authors: Anindita, P.D., Grinkevich, P., Franta, Z.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BM0 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with AMPPNP	+	</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=7bm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bm0 OCA], [https://pdbe.org/7bm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bm0 RCSB], [https://www.ebi.ac.uk/pdbsum/7bm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bm0 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Franta, Z~~]]	+	__TOC__
-	[[Category: ~~Anindita, P.D~~]]	+	</StructureSection>
-	[[Category: Grinkevich, P]]	+	[[Category: Large Structures]]
		+	[[Category: Anindita PD]]
		+	[[Category: Franta Z]]
		+	[[Category: Grinkevich P]]

OCA: Protected "7bm0" [edit=sysop:move=sysop]

2021-01-27T06:35:00Z

Protected "7bm0" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:35, 27 January 2021

OCA: New page: '''Unreleased structure''' The entry 7bm0 is ON HOLD until Paper Publication Authors: Anindita, P.D., Grinkevich, P., Franta, Z. Description: Crystal structure of the tick-borne enceph...

2021-01-27T06:34:59Z

New page: '''Unreleased structure''' The entry 7bm0 is ON HOLD until Paper Publication Authors: Anindita, P.D., Grinkevich, P., Franta, Z. Description: Crystal structure of the tick-borne enceph...

New page

'''Unreleased structure'''

The entry 7bm0 is ON HOLD until Paper Publication

Authors: Anindita, P.D., Grinkevich, P., Franta, Z.

Description: Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with AMPPNP
[[Category: Unreleased Structures]]
[[Category: Franta, Z]]
[[Category: Anindita, P.D]]
[[Category: Grinkevich, P]]