7qka - Revision history

OCA at 17:37, 1 November 2023

2023-11-01T17:37:53Z

←Older revision		Revision as of 17:37, 1 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7qka]] 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=7QKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QKA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qka]] 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=7QKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QKA FirstGlance]. <br>
-	</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=UED:N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide'>UED</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]] 1.8Å</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=UED:N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide'>UED</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=7qka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qka OCA], [https://pdbe.org/7qka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qka RCSB], [https://www.ebi.ac.uk/pdbsum/7qka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qka 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=7qka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qka OCA], [https://pdbe.org/7qka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qka RCSB], [https://www.ebi.ac.uk/pdbsum/7qka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qka ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:48, 28 December 2022

2022-12-28T08:48:06Z

←Older revision		Revision as of 08:48, 28 December 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7qka is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376==
-		+	<StructureSection load='7qka' size='340' side='right'caption='[[7qka]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[7qka]] 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=7QKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QKA FirstGlance]. <br>
-	~~Description~~:	+	</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=UED:N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide'>UED</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7qka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qka OCA], [https://pdbe.org/7qka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qka RCSB], [https://www.ebi.ac.uk/pdbsum/7qka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qka ProSAT]</span></td></tr>
		+	</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__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Beck T]]
		+	[[Category: Boehler H]]
		+	[[Category: Chapman HN]]
		+	[[Category: Cox R]]
		+	[[Category: Ewert W]]
		+	[[Category: Falke S]]
		+	[[Category: Guenther S]]
		+	[[Category: Hauser M]]
		+	[[Category: Hinrichs W]]
		+	[[Category: Karnicar K]]
		+	[[Category: Lach M]]
		+	[[Category: Lieske J]]
		+	[[Category: Lindic N]]
		+	[[Category: Loboda J]]
		+	[[Category: Meents A]]
		+	[[Category: Rahmani Mashhour A]]
		+	[[Category: Reinke PYA]]
		+	[[Category: Turk D]]
		+	[[Category: Usenik A]]

OCA at 01:31, 21 April 2022

2022-04-21T01:31:04Z

←Older revision		Revision as of 01:31, 21 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7qka is ON HOLD	+	The entry 7qka is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 05:47, 19 January 2022

2022-01-19T05:47:43Z

←Older revision		Revision as of 05:47, 19 January 2022
Line 3:		Line 3:
	The entry 7qka is ON HOLD		The entry 7qka is ON HOLD

-	Authors: Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.	+	Authors:

-	Description: ~~Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hinrichs, W]]
-	[[Category: Hauser, M]]
-	[[Category: Beck, T]]
-	[[Category: Ewert, W]]
-	[[Category: Chapman, H.N]]
-	[[Category: Lindic, N]]
-	[[Category: Karnicar, K]]
-	[[Category: Loboda, J]]
-	[[Category: Rahmani Mashhour, A]]
-	[[Category: Lieske, J]]
-	[[Category: Lach, M]]
-	[[Category: Usenik, A]]
-	[[Category: Cox, R]]
-	[[Category: Meents, A]]
-	[[Category: Boehler, H]]
-	[[Category: Turk, D]]
-	[[Category: Falke, S]]
-	[[Category: Guenther, S]]
-	[[Category: Reinke, P.Y.A]]

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

2021-12-29T11:49:32Z

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

←Older revision

Revision as of 11:49, 29 December 2021

OCA: New page: '''Unreleased structure''' The entry 7qka is ON HOLD Authors: Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., L...

2021-12-29T11:49:30Z

New page: '''Unreleased structure''' The entry 7qka is ON HOLD Authors: Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., L...

New page

'''Unreleased structure'''

The entry 7qka is ON HOLD

Authors: Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.

Description: Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376
[[Category: Unreleased Structures]]
[[Category: Hinrichs, W]]
[[Category: Hauser, M]]
[[Category: Beck, T]]
[[Category: Ewert, W]]
[[Category: Chapman, H.N]]
[[Category: Lindic, N]]
[[Category: Karnicar, K]]
[[Category: Loboda, J]]
[[Category: Rahmani Mashhour, A]]
[[Category: Lieske, J]]
[[Category: Lach, M]]
[[Category: Usenik, A]]
[[Category: Cox, R]]
[[Category: Meents, A]]
[[Category: Boehler, H]]
[[Category: Turk, D]]
[[Category: Falke, S]]
[[Category: Guenther, S]]
[[Category: Reinke, P.Y.A]]