2xyv - Revision history

OCA at 08:05, 23 August 2023

OCA — Wed, 23 Aug 2023 08:05:59 GMT

←Older revision		Revision as of 08:05, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='2xyv' size='340' side='right'caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2xyv' size='340' side='right'caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cvhsa Cvhsa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus Severe acute respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.06Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [https://pdbe.org/2xyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [https://www.ebi.ac.uk/pdbsum/2xyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xyv 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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [https://pdbe.org/2xyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [https://www.ebi.ac.uk/pdbsum/2xyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xyv ProSAT]</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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cvhsa]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bouvet, M]]	+	[[Category: Severe acute respiratory syndrome-related coronavirus]]
-	[[Category: Canard, B]]	+	[[Category: Bouvet M]]
-	[[Category: Coutard, B]]	+	[[Category: Canard B]]
-	[[Category: Debarnot, C]]	+	[[Category: Coutard B]]
-	[[Category: Decroly, E]]	+	[[Category: Debarnot C]]
-	[[Category: Ferron, F]]	+	[[Category: Decroly E]]
-	[[Category: Gluais, L]]	+	[[Category: Ferron F]]
-	[[Category: Imbert, I]]	+	[[Category: Gluais L]]
-	[[Category: Lescar, J]]	+	[[Category: Imbert I]]
-	[[Category: Ortiz-Lombardia, M]]	+	[[Category: Lescar J]]
-	[[Category: Papageorgiou, N]]	+	[[Category: Ortiz-Lombardia M]]
-	~~[[Category: Rossmann fold]]~~	+	[[Category: Papageorgiou N]]
-	~~[[Category: Transferase-viral protein complex~~]]	+

OCA at 14:56, 17 November 2021

OCA — Wed, 17 Nov 2021 14:56:52 GMT

←Older revision		Revision as of 14:56, 17 November 2021
Line 3:		Line 3:
	<StructureSection load='2xyv' size='340' side='right'caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2xyv' size='340' side='right'caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cvhsa Cvhsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2XYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cvhsa Cvhsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</div></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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [~~http~~://pdbe.org/2xyv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2xyv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2xyv 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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [https://pdbe.org/2xyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [https://www.ebi.ac.uk/pdbsum/2xyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xyv ProSAT]</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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 13:44, 25 December 2019

OCA — Wed, 25 Dec 2019 13:44:13 GMT

←Older revision		Revision as of 13:44, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of the nsp16 nsp10 SARS coronavirus complex==		==Crystal structure of the nsp16 nsp10 SARS coronavirus complex==
-	<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>	+	<StructureSection load='2xyv' size='340' side='right'caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvhsa Cvhsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvhsa Cvhsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYV FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Cvhsa]]		[[Category: Cvhsa]]
		+	[[Category: Large Structures]]
	[[Category: Bouvet, M]]		[[Category: Bouvet, M]]
	[[Category: Canard, B]]		[[Category: Canard, B]]

OCA at 10:54, 5 August 2016

OCA — Fri, 05 Aug 2016 10:54:06 GMT

←Older revision		Revision as of 10:54, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the nsp16 nsp10 SARS coronavirus complex==		==Crystal structure of the nsp16 nsp10 SARS coronavirus complex==
	<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [http://www.ebi.ac.uk/pdbsum/2xyv PDBsum]</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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [http://pdbe.org/2xyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [http://www.ebi.ac.uk/pdbsum/2xyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xyv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 2xyv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:45, 25 December 2014

OCA — Thu, 25 Dec 2014 01:45:53 GMT

←Older revision		Revision as of 01:45, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvhsa Cvhsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [http://www.ebi.ac.uk/pdbsum/2xyv PDBsum]</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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [http://www.ebi.ac.uk/pdbsum/2xyv PDBsum]</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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cvhsa]]
	[[Category: Bouvet, M]]		[[Category: Bouvet, M]]
	[[Category: Canard, B]]		[[Category: Canard, B]]

OCA at 07:20, 12 November 2014

OCA — Wed, 12 Nov 2014 07:20:58 GMT

←Older revision		Revision as of 07:20, 12 November 2014
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURE OF THE NSP16 NSP10~~ SARS ~~CORONAVIRUS COMPLEX~~==	+	==Crystal structure of the nsp16 nsp10 SARS coronavirus complex==
	<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Sars coronavirus]]~~	+	[[Category: Bouvet, M]]
-	[[Category: Bouvet, M.]]	+	[[Category: Canard, B]]
-	[[Category: Canard, B.]]	+	[[Category: Coutard, B]]
-	[[Category: Coutard, B.]]	+	[[Category: Debarnot, C]]
-	[[Category: Debarnot, C.]]	+	[[Category: Decroly, E]]
-	[[Category: Decroly, E.]]	+	[[Category: Ferron, F]]
-	[[Category: Ferron, F.]]	+	[[Category: Gluais, L]]
-	[[Category: Gluais, L.]]	+	[[Category: Imbert, I]]
-	[[Category: Imbert, I.]]	+	[[Category: Lescar, J]]
-	[[Category: Lescar, J.]]	+	[[Category: Ortiz-Lombardia, M]]
-	[[Category: Ortiz-Lombardia, M.]]	+	[[Category: Papageorgiou, N]]
-	[[Category: Papageorgiou, N.]]	+
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
	[[Category: Transferase-viral protein complex]]		[[Category: Transferase-viral protein complex]]

OCA at 14:16, 3 November 2014

OCA — Mon, 03 Nov 2014 14:16:53 GMT

←Older revision		Revision as of 14:16, 3 November 2014
Line 2:		Line 2:
	<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. <br>	+	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [http://www.ebi.ac.uk/pdbsum/2xyv PDBsum]</span></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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [http://www.ebi.ac.uk/pdbsum/2xyv PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 13:
	Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex.,Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B, Imbert I, Gluais L, Papageorgiou N, Sharff A, Bricogne G, Ortiz-Lombardia M, Lescar J, Canard B PLoS Pathog. 2011 May;7(5):e1002059. Epub 2011 May 26. PMID:21637813<ref>PMID:21637813</ref>		Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex.,Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B, Imbert I, Gluais L, Papageorgiou N, Sharff A, Bricogne G, Ortiz-Lombardia M, Lescar J, Canard B PLoS Pathog. 2011 May;7(5):e1002059. Epub 2011 May 26. PMID:21637813<ref>PMID:21637813</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 32:		Line 31:
	[[Category: Ortiz-Lombardia, M.]]		[[Category: Ortiz-Lombardia, M.]]
	[[Category: Papageorgiou, N.]]		[[Category: Papageorgiou, N.]]
-	[[Category: ~~Rossman~~ fold]]	+	[[Category: Rossmann fold]]
	[[Category: Transferase-viral protein complex]]		[[Category: Transferase-viral protein complex]]

OCA at 07:48, 14 May 2014

OCA — Wed, 14 May 2014 07:48:17 GMT

←Older revision		Revision as of 07:48, 14 May 2014
Line 1:		Line 1:
-	[[~~Image:~~2xyv.~~png~~\|~~left~~\|~~200px~~]]	+	==CRYSTAL STRUCTURE OF THE NSP16 NSP10 SARS CORONAVIRUS COMPLEX==
		+	<StructureSection load='2xyv' size='340' side='right' caption='[[2xyv]], [[Resolution\|resolution]] 2.06Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2xyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2d\|2d2d]], [[2ahm\|2ahm]], [[1p9t\|1p9t]], [[1uk3\|1uk3]], [[2xyr\|2xyr]], [[1wof\|1wof]], [[2amd\|2amd]], [[2a5i\|2a5i]], [[2v6n\|2v6n]], [[2bx4\|2bx4]], [[2acf\|2acf]], [[2xyq\|2xyq]], [[1uk4\|1uk4]], [[1z1i\|1z1i]], [[1o5s\|1o5s]], [[2a5k\|2a5k]], [[2c3s\|2c3s]], [[1sxf\|1sxf]], [[1uj1\|1uj1]], [[1uk2\|1uk2]], [[2amq\|2amq]], [[2bx3\|2bx3]], [[1pa5\|1pa5]], [[1puk\|1puk]], [[1uw7\|1uw7]], [[1p76\|1p76]], [[1q1x\|1q1x]], [[2a5a\|2a5a]], [[1ysy\|1ysy]], [[1z1j\|1z1j]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=2xyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xyv RCSB], [http://www.ebi.ac.uk/pdbsum/2xyv PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2'-O)-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 A resolution, which shows nsp10 bound to nsp16 through a approximately 930 A(2) surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in +RNA viruses.

-	<!--	+	Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex.,Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B, Imbert I, Gluais L, Papageorgiou N, Sharff A, Bricogne G, Ortiz-Lombardia M, Lescar J, Canard B PLoS Pathog. 2011 May;7(5):e1002059. Epub 2011 May 26. PMID:21637813<ref>PMID:21637813</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2xyv"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_2xyv\| PDB=2xyv \| SCENE= }}~~	+

-	~~===CRYSTAL STRUCTURE OF THE NSP16 NSP10 SARS CORONAVIRUS COMPLEX===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21637813}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21637813 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21637813}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2xyv]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021637813<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Sars coronavirus]]		[[Category: Sars coronavirus]]
	[[Category: Bouvet, M.]]		[[Category: Bouvet, M.]]

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

OCA — Sun, 30 Oct 2011 09:17:57 GMT

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

←Older revision

Revision as of 09:17, 30 October 2011

OCA at 09:17, 30 October 2011

OCA — Sun, 30 Oct 2011 09:17:52 GMT

←Older revision		Revision as of 09:17, 30 October 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:2xyv.png\|left\|200px]]

-	The ~~entry 2xyv~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2xyv", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_2xyv\| PDB=2xyv \| SCENE= }}

-	~~Authors: Decroly, E., Debarnot, C., Ferron, F., Bouvet, M., Coutard, B., Imbert, I., Gluais, L., Papageorgiou, N., Ortiz-Lombardia, M., Lescar, J., Canard, B.~~	+	===CRYSTAL STRUCTURE OF THE NSP16 NSP10 SARS CORONAVIRUS COMPLEX===

-	Description: Crystal structure of the nsp16 nsp10 SARS coronavirus complex

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Dec 1 11~~:07:~~04 2010''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21637813}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21637813 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21637813}}
		+
		+	==About this Structure==
		+	[[2xyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYV OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021637813</ref><references group="xtra"/>
		+	[[Category: Sars coronavirus]]
		+	[[Category: Bouvet, M.]]
		+	[[Category: Canard, B.]]
		+	[[Category: Coutard, B.]]
		+	[[Category: Debarnot, C.]]
		+	[[Category: Decroly, E.]]
		+	[[Category: Ferron, F.]]
		+	[[Category: Gluais, L.]]
		+	[[Category: Imbert, I.]]
		+	[[Category: Lescar, J.]]
		+	[[Category: Ortiz-Lombardia, M.]]
		+	[[Category: Papageorgiou, N.]]
		+	[[Category: Rossman fold]]
		+	[[Category: Transferase-viral protein complex]]