2rnk - Revision history

OCA at 09:44, 22 May 2024

2024-05-22T09:44:37Z

←Older revision		Revision as of 09:44, 22 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus Severe acute respiratory syndrome-related coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus Severe acute respiratory syndrome-related coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNK 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=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [https://pdbe.org/2rnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [https://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [https://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [https://pdbe.org/2rnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [https://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [https://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 11:29, 1 February 2023

2023-02-01T11:29:08Z

←Older revision		Revision as of 11:29, 1 February 2023
Line 1:		Line 1:

	==NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3==		==NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3==
-	<StructureSection load='2rnk' size='340' side='right'caption='[[2rnk~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2rnk' size='340' side='right'caption='[[2rnk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus Severe acute respiratory syndrome-related coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNK FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</div></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=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [https://pdbe.org/2rnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [https://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [https://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</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=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [https://pdbe.org/2rnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [https://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [https://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~R1AB_CVHSA R1AB_CVHSA~~]~~] The replicase polyprotein of coronaviruses is a multifunctional~~ protein~~: it contains the activities necessary for~~ the transcription ~~of negative stranded RNA, leader RNA, subgenomic mRNAs~~ and ~~progeny virion RNA as well as~~ proteinases responsible for the ~~cleavage~~ of the polyprotein ~~into functional products (~~By ~~similarity~~).<ref>PMID:~~17024178~~</ref> <ref>PMID:~~17692280~~</ref> <ref>PMID:~~19369340~~</ref> ~~The papain-like proteinase (PL-PRO) is responsible~~ for the cleavages located at the N-terminus of 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. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host ~~IRF~~-3.<ref>PMID:~~17024178~~</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> ~~The main proteinase 3CL~~-~~PRO is responsible~~ for ~~the majority of cleavages as it cleaves~~ the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]~~. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity)~~. Also ~~contains~~ an ADP-ribose-1''-phosphate (ADRP)~~-binding function~~.<ref>PMID:~~17024178~~</ref> <ref>PMID:~~17692280~~</ref> <ref>PMID:~~19369340~~</ref> ~~The helicase which contains~~ a ~~zinc finger structure displays RNA and DNA duplex-unwinding activities~~ with ~~5' to 3' polarity. Its ATPase activity is strongly stimulated by poly~~(U)~~, poly(dT), poly(C), poly(dA), but not~~ by ~~poly(G)~~. ~~Activity of helicase is dependent on magnesium~~.<ref>PMID:~~17024178~~</ref> <ref>PMID:~~17692280~~</ref> <ref>PMID:~~19369340~~</ref> ~~The exoribonuclease acts on both ssRNA and dsRNA in~~ a 3' to 5' ~~direction~~.<ref>PMID:~~17024178~~</ref> <ref>PMID:~~17692280~~</ref> <ref>PMID:~~19369340~~</ref> ~~Nsp7-nsp8 hexadecamer may possibly confer processivity~~ to ~~the polymerase~~, ~~maybe by binding to dsRNA or by producing primers utilized by~~ the ~~latter~~.<ref>PMID:~~17024178~~</ref> <ref>PMID:~~17692280~~</ref> <ref>PMID:~~19369340~~</ref> ~~Nsp9 is a ssRNA-binding protein.~~<ref>PMID:~~17024178~~</ref> <ref>PMID:~~17692280~~</ref> <ref>PMID:~~19369340~~</ref> ~~NendoU is a~~ Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.<ref>PMID:~~17024178~~</ref> <ref>PMID:~~17692280~~</ref> ~~<ref>PMID:19369340</ref>~~	+	[https://www.uniprot.org/uniprot/R1AB_SARS R1AB_SARS] Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein. 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 (PubMed:23035226). May disrupt nuclear pore function by binding and displacing host NUP93 (PubMed:30943371).<ref>PMID:23035226</ref> <ref>PMID:30943371</ref> 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.<ref>PMID:19640993</ref> 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 (PubMed:17692280). Plays a role in host membrane rearrangement that leads to creation of cytoplasmic double-membrane vesicles (DMV) necessary for viral replication. Nsp3, nsp4 and nsp6 together are sufficient to form DMV (PubMed:24410069). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:19369340, PubMed:24622840). Prevents also host NF-kappa-B signaling.<ref>PMID:16271890</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> <ref>PMID:24622840</ref> <ref>PMID:24410069</ref> Plays a role in host membrane rearrangement that leads to creation of cytoplasmic double-membrane vesicles (DMV) necessary for viral replication. Alone appears incapable to induce membrane curvature, but together with nsp3 is able to induce paired membranes. Nsp3, nsp4 and nsp6 together are sufficient to form DMV.<ref>PMID:23943763</ref> <ref>PMID:24410069</ref> Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Also able to bind an ADP-ribose-1''-phosphate (ADRP). May cleave host ATP6V1G1 thereby modifying host vacuoles intracellular pH.[PROSITE-ProRule:PRU00772]<ref>PMID:16226257</ref> Plays a role in host membrane rearrangement that leads to creation of cytoplasmic double-membrane vesicles (DMV) necessary for viral replication. Nsp3, nsp4 and nsp6 together are sufficient to form DMV (PubMed:24410069). 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 (PubMed:24991833).<ref>PMID:24991833</ref> <ref>PMID:24410069</ref> 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.<ref>PMID:22039154</ref> 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.<ref>PMID:22039154</ref> May participate in viral replication by acting as a ssRNA-binding protein.<ref>PMID:19153232</ref> 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.<ref>PMID:22635272</ref> Responsible for replication and transcription of the viral RNA genome.<ref>PMID:22791111</ref> 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.<ref>PMID:12917423</ref> <ref>PMID:22615777</ref> 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 (PubMed:16549795, PubMed:20421945, PubMed:22635272). Acts as a proofreading exoribonuclease for RNA replication, thereby lowering The sensitivity of the virus to RNA mutagens (PubMed:23966862, PubMed:29511076, PubMed:21593585).<ref>PMID:16549795</ref> <ref>PMID:20421945</ref> <ref>PMID:21593585</ref> <ref>PMID:22635272</ref> <ref>PMID:23966862</ref> <ref>PMID:29511076</ref> Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond. 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.<ref>PMID:18417574</ref> <ref>PMID:20421945</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Buchmeier, M J~~]]	+	[[Category: Severe acute respiratory syndrome-related coronavirus]]
-	[[Category: ~~Chatterjee, A~~]]	+	[[Category: Buchmeier MJ]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Chatterjee A]]
-	[[Category: Johnson~~, M A~~]]	+	[[Category: Johnson MA]]
-	[[Category: Joseph, J]]	+	[[Category: Joseph J]]
-	[[Category: Kuhn, P]]	+	[[Category: Kuhn P]]
-	[[Category: Neuman~~, B W~~]]	+	[[Category: Neuman BW]]
-	[[Category: Pedrini, B]]	+	[[Category: Pedrini B]]
-	[[Category: Saikatendu, K]]	+	[[Category: Saikatendu K]]
-	[[Category: Serrano, P]]	+	[[Category: Serrano P]]
-	[[Category: Stevens~~, R C~~]]	+	[[Category: Stevens RC]]
-	[[Category: Wilson~~, I A~~]]	+	[[Category: Wilson IA]]
-	[[Category: Wuthrich, K]]	+	[[Category: Wuthrich K]]
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Fsp]]~~	+
-	~~[[Category: Functional and structural proteomics of sars-cov-related protein]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Jcsg]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nonstructural protein]]~~	+
-	~~[[Category: Nsp3]]~~	+
-	~~[[Category: Nsp3c]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Ribosomal frameshift]]~~	+
-	~~[[Category: Rna replication]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rna-directed rna polymerase]]~~	+
-	~~[[Category: Sars-cov]]~~	+
-	~~[[Category: Sars-unique domain]]~~	+
-	~~[[Category: Thiol protease]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 06:53, 16 March 2022

2022-03-16T06:53:37Z

←Older revision		Revision as of 06:53, 16 March 2022
Line 3:		Line 3:
	<StructureSection load='2rnk' size='340' side='right'caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2rnk' size='340' side='right'caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure ~~with sequence from [https://en.wikipedia.org/wiki/Cvhsa Cvhsa]~~. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</div></td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 CVHSA])</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=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [https://pdbe.org/2rnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [https://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [https://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</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=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [https://pdbe.org/2rnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [https://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [https://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>
	</table>		</table>
Line 36:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cvhsa]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Buchmeier, M J]]		[[Category: Buchmeier, M J]]

OCA at 10:34, 7 July 2021

2021-07-07T10:34:05Z

←Older revision		Revision as of 10:34, 7 July 2021
Line 1:		Line 1:

	==NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3==		==NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3==
-	<StructureSection load='2rnk' size='340' side='right' caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2rnk' size='340' side='right'caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cvhsa Cvhsa]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cvhsa Cvhsa]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RNK FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 CVHSA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 CVHSA])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [~~http~~://pdbe.org/2rnk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [~~http~~://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</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=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [https://pdbe.org/2rnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [https://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [https://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/R1AB_CVHSA R1AB_CVHSA]] The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products (By similarity).<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of 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. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity). Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G). Activity of helicase is dependent on magnesium.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> Nsp9 is a ssRNA-binding protein.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref>	+	[[https://www.uniprot.org/uniprot/R1AB_CVHSA R1AB_CVHSA]] The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products (By similarity).<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of 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. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity). Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G). Activity of helicase is dependent on magnesium.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> Nsp9 is a ssRNA-binding protein.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Nonstructural protein\|Nonstructural protein]]	+	*[[Nonstructural protein 3D structures\|Nonstructural protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Cvhsa]]		[[Category: Cvhsa]]
		+	[[Category: Large Structures]]
	[[Category: Buchmeier, M J]]		[[Category: Buchmeier, M J]]
	[[Category: Chatterjee, A]]		[[Category: Chatterjee, A]]

OCA at 10:51, 5 September 2018

2018-09-05T10:51:35Z

←Older revision		Revision as of 10:51, 5 September 2018
Line 1:		Line 1:
		+
	==NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3==		==NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3==
	<StructureSection load='2rnk' size='340' side='right' caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2rnk' size='340' side='right' caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 CVHSA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 CVHSA])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [http://pdbe.org/2rnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [http://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [http://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [http://pdbe.org/2rnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [http://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rnk ProSAT], [http://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rn/2rnk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rn/2rnk_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 50:		Line 51:
	[[Category: Wuthrich, K]]		[[Category: Wuthrich, K]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
		+	[[Category: Cytoplasm]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
Line 77:		Line 79:
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
		+	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

OCA at 12:39, 8 February 2016

2016-02-08T12:39:04Z

←Older revision		Revision as of 12:39, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2rnk' size='340' side='right' caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2rnk' size='340' side='right' caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sars_coronavirus Sars coronavirus~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvhsa Cvhsa]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RNK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 ~~SARS coronavirus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 CVHSA])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [http://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [http://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [http://pdbe.org/2rnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [http://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [http://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rnk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2rnk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sars coronavirus~~]]	+	[[Category: Cvhsa]]
	[[Category: Buchmeier, M J]]		[[Category: Buchmeier, M J]]
	[[Category: Chatterjee, A]]		[[Category: Chatterjee, A]]

OCA at 23:22, 24 December 2014

2014-12-24T23:22:52Z

←Older revision		Revision as of 23:22, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RNK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RNK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 SARS coronavirus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 SARS coronavirus])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [http://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [http://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [http://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [http://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/R1AB_CVHSA R1AB_CVHSA]] The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products (By similarity).<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of 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. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity). Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G). Activity of helicase is dependent on magnesium.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> Nsp9 is a ssRNA-binding protein.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref> NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.<ref>PMID:17024178</ref> <ref>PMID:17692280</ref> <ref>PMID:19369340</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Sars coronavirus]]		[[Category: Sars coronavirus]]
-	[[Category: Buchmeier, M J.]]	+	[[Category: Buchmeier, M J]]
-	[[Category: Chatterjee, A.]]	+	[[Category: Chatterjee, A]]
-	[[Category: ~~JCSG, Joint Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Johnson, M A.]]	+	[[Category: Johnson, M A]]
-	[[Category: Joseph, J.]]	+	[[Category: Joseph, J]]
-	[[Category: Kuhn, P.]]	+	[[Category: Kuhn, P]]
-	[[Category: Neuman, B W.]]	+	[[Category: Neuman, B W]]
-	[[Category: Pedrini, B.]]	+	[[Category: Pedrini, B]]
-	[[Category: Saikatendu, K.]]	+	[[Category: Saikatendu, K]]
-	[[Category: Serrano, P.]]	+	[[Category: Serrano, P]]
-	[[Category: Stevens, R C.]]	+	[[Category: Stevens, R C]]
-	[[Category: Wilson, I A.]]	+	[[Category: Wilson, I A]]
-	[[Category: Wuthrich, K.]]	+	[[Category: Wuthrich, K]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
Line 54:		Line 56:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Jcsg]]		[[Category: Jcsg]]
-	[[Category: Joint center for structural genomic]]
	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
Line 64:		Line 65:
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
	[[Category: Protease]]		[[Category: Protease]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi-2~~]]	+
	[[Category: Ribosomal frameshift]]		[[Category: Ribosomal frameshift]]
	[[Category: Rna replication]]		[[Category: Rna replication]]

OCA at 08:25, 29 September 2014

2014-09-29T08:25:05Z

←Older revision		Revision as of 08:25, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rnk.~~png~~\|~~left~~\|200px]]	+	==NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3==
		+	<StructureSection load='2rnk' size='340' side='right' caption='[[2rnk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rnk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RNK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jzf\|2jzf]], [[2jzd\|2jzd]], [[2jze\|2jze]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 SARS coronavirus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rnk RCSB], [http://www.ebi.ac.uk/pdbsum/2rnk PDBsum], [http://www.topsan.org/Proteins/JCSG/2rnk TOPSAN]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rn/2rnk_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

-	~~{{STRUCTURE_2rnk\| PDB=2rnk \| SCENE= }}~~	+	Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.,Chatterjee A, Johnson MA, Serrano P, Pedrini B, Joseph JS, Neuman BW, Saikatendu K, Buchmeier MJ, Kuhn P, Wuthrich K J Virol. 2009 Feb;83(4):1823-36. Epub 2008 Dec 3. PMID:19052085<ref>PMID:19052085</ref>

-	~~===NMR structure~~ of the ~~domain 513-651 of the SARS-CoV nonstructural protein nsp3===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19052085}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2rnk]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sars_coronavirus Sars coronavirus]~~. ~~This structure supersedes the now removed PDB entry [http:~~/~~/oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA].~~	+

	==See Also==		==See Also==
	*[[Nonstructural protein\|Nonstructural protein]]		*[[Nonstructural protein\|Nonstructural protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019052085<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Sars coronavirus]]		[[Category: Sars coronavirus]]
	[[Category: Buchmeier, M J.]]		[[Category: Buchmeier, M J.]]

OCA at 10:09, 20 October 2012

2012-10-20T10:09:27Z

←Older revision		Revision as of 10:09, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[2rnk]] is a 1 chain structure ~~of [[Nonstructural protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA].	+	[[2rnk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jwi 2jwi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNK OCA].

	==See Also==		==See Also==

OCA: Protected "2rnk" [edit=sysop:move=sysop]

2012-07-26T01:10:21Z

Protected "2rnk" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:10, 26 July 2012