5sr4 - Revision history

OCA at 18:07, 20 September 2023

OCA — Wed, 20 Sep 2023 18:07:30 GMT

←Older revision		Revision as of 18:07, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5sr4]] 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=5SR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SR4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5sr4]] 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=5SR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SR4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QYO:(1S,3R)-3-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]cyclopentan-1-ol'>QYO</scene>, <scene name='pdbligand=QYU:(1R,3S)-3-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]cyclopentan-1-ol'>QYU</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]] 1.05Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QYO:(1S,3R)-3-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]cyclopentan-1-ol'>QYO</scene>, <scene name='pdbligand=QYU:(1R,3S)-3-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]cyclopentan-1-ol'>QYU</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=5sr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sr4 OCA], [https://pdbe.org/5sr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sr4 RCSB], [https://www.ebi.ac.uk/pdbsum/5sr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sr4 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=5sr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sr4 OCA], [https://pdbe.org/5sr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sr4 RCSB], [https://www.ebi.ac.uk/pdbsum/5sr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sr4 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:20, 26 October 2022

OCA — Wed, 26 Oct 2022 06:20:23 GMT

←Older revision		Revision as of 06:20, 26 October 2022
Line 8:		Line 8:
	</table>		</table>
	== Function ==		== 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]	+	[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 ==
	<references/>		<references/>

OCA at 06:33, 8 September 2022

OCA — Thu, 08 Sep 2022 06:33:01 GMT

←Older revision		Revision as of 06:33, 8 September 2022
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2479779298 - (R,S) and (S,R) isomers==		==PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2479779298 - (R,S) and (S,R) isomers==
-	<StructureSection load='5sr4' size='340' side='right'caption='[[5sr4]]' scene=''>	+	<StructureSection load='5sr4' size='340' side='right'caption='[[5sr4]], [[Resolution\|resolution]] 1.05Å' 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=5SR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5sr4]] 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=5SR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SR4 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=5sr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sr4 OCA], [https://pdbe.org/5sr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sr4 RCSB], [https://www.ebi.ac.uk/pdbsum/5sr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sr4 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QYO:(1S,3R)-3-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]cyclopentan-1-ol'>QYO</scene>, <scene name='pdbligand=QYU:(1R,3S)-3-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]cyclopentan-1-ol'>QYU</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=5sr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sr4 OCA], [https://pdbe.org/5sr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sr4 RCSB], [https://www.ebi.ac.uk/pdbsum/5sr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sr4 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: Correy GJ]]		[[Category: Correy GJ]]
	[[Category: Fraser JS]]		[[Category: Fraser JS]]

OCA at 16:09, 6 July 2022

OCA — Wed, 06 Jul 2022 16:09:09 GMT

←Older revision		Revision as of 16:09, 6 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5sr4 is ON HOLD~~	+	==PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2479779298 - (R,S) and (S,R) isomers==
-		+	<StructureSection load='5sr4' size='340' side='right'caption='[[5sr4]]' scene=''>
-	~~Authors: Correy, G.J., Fraser, J.S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SR4 FirstGlance]. <br>
-	~~Description:~~ PanDDA analysis group deposition --Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2479779298	+	</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=5sr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sr4 OCA], [https://pdbe.org/5sr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sr4 RCSB], [https://www.ebi.ac.uk/pdbsum/5sr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sr4 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Correy~~, G.J~~]]	+	__TOC__
-	[[Category: Fraser~~, J.S~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Correy GJ]]
		+	[[Category: Fraser JS]]

OCA at 05:58, 29 June 2022

OCA — Wed, 29 Jun 2022 05:58:15 GMT

←Older revision		Revision as of 05:58, 29 June 2022
Line 3:		Line 3:
	The entry 5sr4 is ON HOLD		The entry 5sr4 is ON HOLD

-	Authors: Correy, G.J, Fraser, J.S	+	Authors: Correy, G.J., Fraser, J.S.

	Description: PanDDA analysis group deposition --Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2479779298		Description: PanDDA analysis group deposition --Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2479779298
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Correy, G.J, Fraser, J.S]]	+	[[Category: Correy, G.J]]
		+	[[Category: Fraser, J.S]]

OCA: Protected "5sr4" [edit=sysop:move=sysop]

OCA — Wed, 15 Jun 2022 03:45:59 GMT

Protected "5sr4" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:45, 15 June 2022

OCA: New page: '''Unreleased structure''' The entry 5sr4 is ON HOLD Authors: Correy, G.J, Fraser, J.S Description: PanDDA analysis group deposition --Crystal structure of SARS-CoV-2 NSP3 macrodomain ...

OCA — Wed, 15 Jun 2022 03:45:58 GMT

New page: '''Unreleased structure''' The entry 5sr4 is ON HOLD Authors: Correy, G.J, Fraser, J.S Description: PanDDA analysis group deposition --Crystal structure of SARS-CoV-2 NSP3 macrodomain ...

New page

'''Unreleased structure'''

The entry 5sr4 is ON HOLD

Authors: Correy, G.J, Fraser, J.S

Description: PanDDA analysis group deposition --Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2479779298
[[Category: Unreleased Structures]]
[[Category: Correy, G.J, Fraser, J.S]]