5s3t - Revision history

OCA at 14:12, 6 March 2024

2024-03-06T14:12:17Z

←Older revision		Revision as of 14:12, 6 March 2024
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	==PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with POB0128==		==PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with POB0128==
-	<StructureSection load='5s3t' size='340' side='right'caption='[[5s3t]]' scene=''>	+	<StructureSection load='5s3t' size='340' side='right'caption='[[5s3t]], [[Resolution\|resolution]] 1.08Å' 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=5S3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5S3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5s3t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5S3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5S3T 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=5s3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5s3t OCA], [https://pdbe.org/5s3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5s3t RCSB], [https://www.ebi.ac.uk/pdbsum/5s3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5s3t ProSAT]</span></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]] 1.085Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=W2G:(1R,2S)-2-(thiophen-3-yl)cyclopentane-1-carboxylic+acid'>W2G</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=5s3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5s3t OCA], [https://pdbe.org/5s3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5s3t RCSB], [https://www.ebi.ac.uk/pdbsum/5s3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5s3t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/R1AB_SARS2 R1AB_SARS2] Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.[UniProtKB:P0C6X7] Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.[UniProtKB:P0C6X7] May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.[UniProtKB:P0C6X7] Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.[UniProtKB:P0C6X7] Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.[UniProtKB:P0C6X7] Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN] (PubMed:32198291). Also able to bind an ADP-ribose-1''-phosphate (ADRP).[UniProtKB:P0C6X7]<ref>PMID:32198291</ref> Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] May participate in viral replication by acting as a ssRNA-binding protein.[UniProtKB:P0C6X7] Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.[UniProtKB:P0C6X7] Responsible for replication and transcription of the viral RNA genome.[UniProtKB:P0C6X7] Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium.[UniProtKB:P0C6X7] Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity. Acts as a proofreading exoribonuclease for RNA replication, thereby lowering The sensitivity of the virus to RNA mutagens.[UniProtKB:P0C6X7] Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.[UniProtKB:P0C6X7] Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs. N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system.[UniProtKB:P0C6X7]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
	[[Category: Ahel I]]		[[Category: Ahel I]]
	[[Category: Aimon A]]		[[Category: Aimon A]]

OCA at 10:03, 7 July 2021

2021-07-07T10:03:38Z

←Older revision		Revision as of 10:03, 7 July 2021
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	<StructureSection load='5s3t' size='340' side='right'caption='[[5s3t]]' scene=''>		<StructureSection load='5s3t' size='340' side='right'caption='[[5s3t]]' 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=5S3T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5S3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5S3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5S3T FirstGlance]. <br>
-	</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=5s3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5s3t OCA], [~~http~~://pdbe.org/5s3t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5s3t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5s3t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5s3t ProSAT]</span></td></tr>	+	</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=5s3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5s3t OCA], [https://pdbe.org/5s3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5s3t RCSB], [https://www.ebi.ac.uk/pdbsum/5s3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5s3t ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 05:44, 20 January 2021

2021-01-20T05:44:13Z

←Older revision		Revision as of 05:44, 20 January 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5s3t ~~is ON HOLD~~	+	==PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with POB0128==
-		+	<StructureSection load='5s3t' size='340' side='right'caption='[[5s3t]]' scene=''>
-	~~Authors~~: ~~Fearon, D~~.~~, Schuller, M~~.~~, Rangel, V~~.L.~~, Douangamath, A~~.~~, Rack, J~~.G.M.~~, Zhu, K~~., ~~Aimon, A~~.~~, Brandao-Neto, J~~.~~, Dias, A~~.~~, Dunnet, L., Gorrie~~-~~Stone~~, ~~T.J~~., ~~Powell, A~~.J.~~, Krojer, T~~., ~~Skyner, R~~.~~, Thompson, W~~.~~, Ahel, I~~., ~~von Delft, F~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5S3T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5S3T FirstGlance]. <br>
-	~~Description: PanDDA analysis group deposition --Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with POB0128~~	+	</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=5s3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5s3t OCA], [http://pdbe.org/5s3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5s3t RCSB], [http://www.ebi.ac.uk/pdbsum/5s3t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5s3t ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Aimon, A~~]]	+	__TOC__
-	[[Category: ~~Rangel, V.L~~]]	+	</StructureSection>
-	[[Category: Brandao-Neto, J]]	+	[[Category: Large Structures]]
-	[[Category: ~~Rack, J.G.M~~]]	+	[[Category: Ahel I]]
-	[[Category: ~~Fearon, D~~]]	+	[[Category: Aimon A]]
-	[[Category: ~~Thompson, W~~]]	+	[[Category: Brandao-Neto J]]
-	[[Category: ~~Von Delft, F~~]]	+	[[Category: Dias A]]
-	[[Category: ~~Powell, A.J~~]]	+	[[Category: Douangamath A]]
-	[[Category: ~~Ahel, I~~]]	+	[[Category: Dunnet L]]
-	[[Category: ~~Zhu, K~~]]	+	[[Category: Fearon D]]
-	[[Category: ~~Dunnet, L~~]]	+	[[Category: Gorrie-Stone TJ]]
-	[[Category: ~~Skyner, R~~]]	+	[[Category: Krojer T]]
-	[[Category: ~~Douangamath, A~~]]	+	[[Category: Powell AJ]]
-	[[Category: ~~Krojer, T~~]]	+	[[Category: Rack JGM]]
-	[[Category: ~~Schuller, M~~]]	+	[[Category: Rangel VL]]
-	[[Category: ~~Gorrie-Stone, T.J~~]]	+	[[Category: Schuller M]]
-	[[Category: ~~Dias, A~~]]	+	[[Category: Skyner R]]
		+	[[Category: Thompson W]]
		+	[[Category: Zhu K]]
		+	[[Category: Von Delft F]]

OCA: Protected "5s3t" [edit=sysop:move=sysop]

2020-11-11T06:07:52Z

Protected "5s3t" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:07, 11 November 2020

OCA: New page: '''Unreleased structure''' The entry 5s3t is ON HOLD Authors: Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Rack, J.G.M., Zhu, K., Aimon, A., Brandao-Neto, J., Dias, A., Dunn...

2020-11-11T06:07:51Z

New page: '''Unreleased structure''' The entry 5s3t is ON HOLD Authors: Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Rack, J.G.M., Zhu, K., Aimon, A., Brandao-Neto, J., Dias, A., Dunn...

New page

'''Unreleased structure'''

The entry 5s3t is ON HOLD

Authors: Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Rack, J.G.M., Zhu, K., Aimon, A., Brandao-Neto, J., Dias, A., Dunnet, L., Gorrie-Stone, T.J., Powell, A.J., Krojer, T., Skyner, R., Thompson, W., Ahel, I., von Delft, F.

Description: PanDDA analysis group deposition --Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with POB0128
[[Category: Unreleased Structures]]
[[Category: Aimon, A]]
[[Category: Rangel, V.L]]
[[Category: Brandao-Neto, J]]
[[Category: Rack, J.G.M]]
[[Category: Fearon, D]]
[[Category: Thompson, W]]
[[Category: Von Delft, F]]
[[Category: Powell, A.J]]
[[Category: Ahel, I]]
[[Category: Zhu, K]]
[[Category: Dunnet, L]]
[[Category: Skyner, R]]
[[Category: Douangamath, A]]
[[Category: Krojer, T]]
[[Category: Schuller, M]]
[[Category: Gorrie-Stone, T.J]]
[[Category: Dias, A]]