OCA at 14:10, 6 March 2024

2024-03-06T14:10:02Z

←Older revision		Revision as of 14:10, 6 March 2024
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5s2d ~~is ON HOLD~~	+	==PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z369936976==
-		+	<StructureSection load='5s2d' size='340' side='right'caption='[[5s2d]], [[Resolution\|resolution]] 1.06Å' 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'>[[5s2d]] 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=5S2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5S2D FirstGlance]. <br>
-	~~Description~~: ~~PanDDA analysis group deposition~~ --~~Crystal Structure~~ of ~~SARS-CoV~~-~~2 Nsp3 macrodomain~~ in ~~complex with Z369936976~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.06Å</td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U0P:N-cyclopropyl-N-methyl-N-[(5-methyl-1,2-oxazol-3-yl)methyl]urea'>U0P</scene></td></tr>
-	[[Category: ~~Aimon, A~~]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5s2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5s2d OCA], [https://pdbe.org/5s2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5s2d RCSB], [https://www.ebi.ac.uk/pdbsum/5s2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5s2d ProSAT]</span></td></tr>
-	[[Category: ~~Rangel, V.L~~]]	+	</table>
-	[[Category: Brandao-Neto, J]]	+	== Function ==
-	[[Category: ~~Rack, J.G.M~~]]	+	[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]
-	[[Category: ~~Fearon, D~~]]	+	== References ==
-	[[Category: ~~Thompson, W~~]]	+	<references/>
-	[[Category: ~~Von Delft, F~~]]	+	__TOC__
-	[[Category: ~~Powell, A.J~~]]	+	</StructureSection>
-	[[Category: ~~Ahel, I~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Zhu, K~~]]	+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
-	[[Category: ~~Dunnet, L~~]]	+	[[Category: Ahel I]]
-	[[Category: ~~Skyner, R~~]]	+	[[Category: Aimon A]]
-	[[Category: ~~Douangamath, A~~]]	+	[[Category: Brandao-Neto J]]
-	[[Category: ~~Krojer, T~~]]	+	[[Category: Dias A]]
-	[[Category: ~~Schuller, M~~]]	+	[[Category: Douangamath A]]
-	[[Category: ~~Gorrie-Stone, T.J~~]]	+	[[Category: Dunnet L]]
-	[[Category: ~~Dias, A~~]]	+	[[Category: Fearon D]]
		+	[[Category: Gorrie-Stone TJ]]
		+	[[Category: Krojer T]]
		+	[[Category: Powell AJ]]
		+	[[Category: Rack JGM]]
		+	[[Category: Rangel VL]]
		+	[[Category: Schuller M]]
		+	[[Category: Skyner R]]
		+	[[Category: Thompson W]]
		+	[[Category: Zhu K]]
		+	[[Category: Von Delft F]]

OCA: Protected "5s2d" [edit=sysop:move=sysop]

2020-11-11T06:02:00Z

Protected "5s2d" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:02, 11 November 2020

OCA: New page: '''Unreleased structure''' The entry 5s2d 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...

2020-11-11T06:01:58Z

New page: '''Unreleased structure''' The entry 5s2d 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 5s2d 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 Z369936976
[[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]]

5s2d - Revision history

OCA at 14:10, 6 March 2024

OCA: Protected "5s2d" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 5s2d 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...