7kag - Revision history

OCA at 15:20, 18 October 2023

OCA — Wed, 18 Oct 2023 15:20:25 GMT

←Older revision		Revision as of 15:20, 18 October 2023
Line 1:		Line 1:

	==Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2==		==Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2==
-	<StructureSection load='7kag' size='340' side='right'caption='[[7kag]]' scene=''>	+	<StructureSection load='7kag' size='340' side='right'caption='[[7kag]], [[Resolution\|resolution]] 3.21Å' 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=7KAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kag]] 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=7KAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KAG 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=7kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kag OCA], [https://pdbe.org/7kag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kag RCSB], [https://www.ebi.ac.uk/pdbsum/7kag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kag 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]] 3.21Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kag OCA], [https://pdbe.org/7kag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kag RCSB], [https://www.ebi.ac.uk/pdbsum/7kag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kag 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]

	==See Also==		==See Also==
	*[[Nonstructural protein 3D structures\|Nonstructural protein 3D structures]]		*[[Nonstructural protein 3D structures\|Nonstructural protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
	[[Category: Chang C]]		[[Category: Chang C]]
	[[Category: Di Leo R]]		[[Category: Di Leo R]]

OCA at 07:08, 27 January 2022

OCA — Thu, 27 Jan 2022 07:08:29 GMT

←Older revision		Revision as of 07:08, 27 January 2022
Line 3:		Line 3:
	<StructureSection load='7kag' size='340' side='right'caption='[[7kag]]' scene=''>		<StructureSection load='7kag' size='340' side='right'caption='[[7kag]]' 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=7KAG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7KAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KAG 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=7kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kag OCA], [~~http~~://pdbe.org/7kag PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7kag RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7kag PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7kag 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=7kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kag OCA], [https://pdbe.org/7kag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kag RCSB], [https://www.ebi.ac.uk/pdbsum/7kag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kag ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Nonstructural protein 3D structures\|Nonstructural protein 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:53, 14 October 2020

OCA — Wed, 14 Oct 2020 05:53:20 GMT

←Older revision		Revision as of 05:53, 14 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7kag ~~is ON HOLD~~	+	==Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2==
-		+	<StructureSection load='7kag' size='340' side='right'caption='[[7kag]]' scene=''>
-	~~Authors~~: ~~Stogios, P~~.J.~~, Skarina, T~~.~~, Chang, C~~.~~, Kim, Y~~.~~, Di Leo, R~~., ~~Savchenko, A~~., ~~Joachimiak, A~~., ~~Satchell~~, K.J.F., ~~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=7KAG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7KAG FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the ubiquitin~~-~~like domain from Nsp3 from SARS-CoV-2~~	+	</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=7kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kag OCA], [http://pdbe.org/7kag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7kag RCSB], [http://www.ebi.ac.uk/pdbsum/7kag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7kag ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Joachimiak, A~~]]	+	__TOC__
-	[[Category: ~~Skarina, T~~]]	+	</StructureSection>
-	[[Category: ~~Di Leo, R~~]]	+	[[Category: Large Structures]]
-	[[Category: Kim, Y]]	+	[[Category: Chang C]]
-	[[Category: ~~Chang, C~~]]	+	[[Category: Di Leo R]]
-	[[Category: Savchenko, A]]	+	[[Category: Joachimiak A]]
-	[[Category: ~~Stogios, P.J~~]]	+	[[Category: Kim Y]]
-	[[Category: ~~Satchell, K.J.F]]~~	+	[[Category: Satchell KJF]]
-	~~[[Category: Center For Structural Genomics Of Infectious Diseases (Csgid)~~]]	+	[[Category: Savchenko A]]
		+	[[Category: Skarina T]]
		+	[[Category: Stogios PJ]]

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

OCA — Wed, 07 Oct 2020 04:51:24 GMT

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

←Older revision

Revision as of 04:51, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7kag is ON HOLD Authors: Stogios, P.J., Skarina, T., Chang, C., Kim, Y., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Str...

OCA — Wed, 07 Oct 2020 04:51:22 GMT

New page: '''Unreleased structure''' The entry 7kag is ON HOLD Authors: Stogios, P.J., Skarina, T., Chang, C., Kim, Y., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Str...

New page

'''Unreleased structure'''

The entry 7kag is ON HOLD

Authors: Stogios, P.J., Skarina, T., Chang, C., Kim, Y., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Description: Crystal structure of the ubiquitin-like domain from Nsp3 from SARS-CoV-2
[[Category: Unreleased Structures]]
[[Category: Joachimiak, A]]
[[Category: Skarina, T]]
[[Category: Di Leo, R]]
[[Category: Kim, Y]]
[[Category: Chang, C]]
[[Category: Savchenko, A]]
[[Category: Stogios, P.J]]
[[Category: Satchell, K.J.F]]
[[Category: Center For Structural Genomics Of Infectious Diseases (Csgid)]]