7koj - Revision history

OCA at 15:29, 18 October 2023

OCA — Wed, 18 Oct 2023 15:29:09 GMT

←Older revision		Revision as of 15:29, 18 October 2023
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-	==The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494==	+	==The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494 inhibitor==
-	<StructureSection load='7koj' size='340' side='right'caption='[[7koj]]' scene=''>	+	<StructureSection load='7koj' size='340' side='right'caption='[[7koj]], [[Resolution\|resolution]] 2.02Å' 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=7KOJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KOJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7koj]] 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=7KOJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KOJ 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=7koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7koj OCA], [https://pdbe.org/7koj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7koj RCSB], [https://www.ebi.ac.uk/pdbsum/7koj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7koj 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]] 2.02Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=Y94:2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]-5-{[(prop-2-en-1-yl)carbamoyl]amino}benzamide'>Y94</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=7koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7koj OCA], [https://pdbe.org/7koj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7koj RCSB], [https://www.ebi.ac.uk/pdbsum/7koj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7koj 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: Azizi SA]]		[[Category: Azizi SA]]
	[[Category: Dickinson BC]]		[[Category: Dickinson BC]]

OCA at 10:51, 31 March 2021

OCA — Wed, 31 Mar 2021 10:51:29 GMT

←Older revision		Revision as of 10:51, 31 March 2021
Line 3:		Line 3:
	<StructureSection load='7koj' size='340' side='right'caption='[[7koj]]' scene=''>		<StructureSection load='7koj' size='340' side='right'caption='[[7koj]]' 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=7KOJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7KOJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KOJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KOJ 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=7koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7koj OCA], [~~http~~://pdbe.org/7koj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7koj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7koj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7koj 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=7koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7koj OCA], [https://pdbe.org/7koj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7koj RCSB], [https://www.ebi.ac.uk/pdbsum/7koj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7koj ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

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

OCA — Wed, 18 Nov 2020 09:42:19 GMT

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

←Older revision

Revision as of 09:42, 18 November 2020

OCA: New page: ==The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494==
OCA — Wed, 18 Nov 2020 09:42:18 GMT

New page: ==The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494== <StructureSection load='7koj' size='340' side='right'caption='7koj' scene=...

New page

==The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494==
<StructureSection load='7koj' size='340' side='right'caption='[[7koj]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KOJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7KOJ 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=7koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7koj OCA], [http://pdbe.org/7koj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7koj RCSB], [http://www.ebi.ac.uk/pdbsum/7koj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7koj ProSAT]</span></td></tr>
</table>
TOC
</StructureSection>
[[Category: Large Structures]]
[[Category: Azizi SA]]
[[Category: Dickinson BC]]
[[Category: Endres M]]
[[Category: Joachimiak A]]
[[Category: Jones K]]
[[Category: Kathayat R]]
[[Category: Lisnyak V]]
[[Category: Maki S]]
[[Category: Osipiuk J]]
[[Category: Snyder SA]]
[[Category: Taylor C]]
[[Category: Tesar C]]
[[Category: Zhang Y]]
[[Category: Zhou Z]]