6wzu - Revision history

OCA at 14:39, 18 October 2023

OCA — Wed, 18 Oct 2023 14:39:44 GMT

←Older revision		Revision as of 14:39, 18 October 2023
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	==The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group==		==The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group==
-	<StructureSection load='6wzu' size='340' side='right'caption='[[6wzu]]' scene=''>	+	<StructureSection load='6wzu' size='340' side='right'caption='[[6wzu]], [[Resolution\|resolution]] 1.79Å' 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=6WZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wzu]] is a 1 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=6WZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WZU 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=6wzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wzu OCA], [https://pdbe.org/6wzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wzu RCSB], [https://www.ebi.ac.uk/pdbsum/6wzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wzu 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]] 1.79Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=6wzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wzu OCA], [https://pdbe.org/6wzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wzu RCSB], [https://www.ebi.ac.uk/pdbsum/6wzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wzu 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]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to expand. Papain-like protease (PLpro) is one of two SARS-CoV-2 proteases potentially targetable with antivirals. PLpro is an attractive target because it plays an essential role in cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex, and disruption of host responses. We report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the SARS-CoV-2 enzyme. We determined the high resolution structure of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors. This collection of structures details inhibitors recognition and interactions providing fundamental molecular and mechanistic insight into PLpro. All compounds inhibit the peptidase activity of PLpro in vitro, some block SARS-CoV-2 replication in cell culture assays. These findings will accelerate structure-based drug design efforts targeting PLpro to identify high-affinity inhibitors of clinical value.
		+
		+	Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.,Osipiuk J, Azizi SA, Dvorkin S, Endres M, Jedrzejczak R, Jones KA, Kang S, Kathayat RS, Kim Y, Lisnyak VG, Maki SL, Nicolaescu V, Taylor CA, Tesar C, Zhang YA, Zhou Z, Randall G, Michalska K, Snyder SA, Dickinson BC, Joachimiak A Nat Commun. 2021 Feb 2;12(1):743. doi: 10.1038/s41467-021-21060-3. PMID:33531496<ref>PMID:33531496</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wzu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
	[[Category: Endres M]]		[[Category: Endres M]]
	[[Category: Jedrzejczak R]]		[[Category: Jedrzejczak R]]

OCA at 11:08, 10 February 2021

OCA — Wed, 10 Feb 2021 11:08:10 GMT

←Older revision		Revision as of 11:08, 10 February 2021
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	<StructureSection load='6wzu' size='340' side='right'caption='[[6wzu]]' scene=''>		<StructureSection load='6wzu' size='340' side='right'caption='[[6wzu]]' 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=6WZU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WZU 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=6wzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wzu OCA], [~~http~~://pdbe.org/6wzu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wzu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wzu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wzu 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=6wzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wzu OCA], [https://pdbe.org/6wzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wzu RCSB], [https://www.ebi.ac.uk/pdbsum/6wzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wzu ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 07:04, 27 May 2020

OCA — Wed, 27 May 2020 07:04:02 GMT

←Older revision		Revision as of 07:04, 27 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6wzu is ON HOLD~~	+	==The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group==
-		+	<StructureSection load='6wzu' size='340' side='right'caption='[[6wzu]]' scene=''>
-	~~Authors: Osipiuk, J., Tesar, C., Endres, M., Jedrzejczak, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WZU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WZU FirstGlance]. <br>
-	~~Description:~~ The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group	+	</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=6wzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wzu OCA], [http://pdbe.org/6wzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wzu RCSB], [http://www.ebi.ac.uk/pdbsum/6wzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wzu ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Tesar~~, C]]	+	__TOC__
-	[[Category: ~~Jedrzejczak, R~~]]	+	</StructureSection>
-	[[Category: ~~Osipiuk, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Center For Structural Genomics Of Infectious Diseases (Csgid)~~]]	+	[[Category: Endres M]]
-	[[Category: Joachimiak, A]]	+	[[Category: Jedrzejczak R]]
-	[[Category: ~~Endres, M~~]]	+	[[Category: Joachimiak A]]
		+	[[Category: Osipiuk J]]
		+	[[Category: Tesar C]]

OCA: Protected "6wzu" [edit=sysop:move=sysop]

OCA — Wed, 20 May 2020 04:25:02 GMT

Protected "6wzu" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:25, 20 May 2020

OCA: New page: '''Unreleased structure''' The entry 6wzu is ON HOLD Authors: Osipiuk, J., Tesar, C., Endres, M., Jedrzejczak, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases ...

OCA — Wed, 20 May 2020 04:25:00 GMT

New page: '''Unreleased structure''' The entry 6wzu is ON HOLD Authors: Osipiuk, J., Tesar, C., Endres, M., Jedrzejczak, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases ...

New page

'''Unreleased structure'''

The entry 6wzu is ON HOLD

Authors: Osipiuk, J., Tesar, C., Endres, M., Jedrzejczak, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Description: The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group
[[Category: Unreleased Structures]]
[[Category: Tesar, C]]
[[Category: Jedrzejczak, R]]
[[Category: Osipiuk, J]]
[[Category: Center For Structural Genomics Of Infectious Diseases (Csgid)]]
[[Category: Joachimiak, A]]
[[Category: Endres, M]]