2z9j - Revision history

OCA at 13:27, 1 November 2023

OCA — Wed, 01 Nov 2023 13:27:10 GMT

←Older revision		Revision as of 13:27, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2z9j' size='340' side='right'caption='[[2z9j]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2z9j' size='340' side='right'caption='[[2z9j]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>~~, ~~<scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.95Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[2z9g\|2z9g]]~~, ~~[[2z9k\|2z9k]], [[2z9l\|2z9l]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [~~http~~://pdbe.org/2z9j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z9j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9j 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=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [https://pdbe.org/2z9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [https://www.ebi.ac.uk/pdbsum/2z9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9j 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_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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	==See Also==		==See Also==
-	*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]	+	*[[Virus protease 3D structures\|Virus protease 3D structures]]
-	*[[Virus ~~proteases~~ 3D ~~strutures~~\|Virus ~~proteases~~ 3D ~~strutures~~]]	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cvhsa]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lee, C C]]~~	+	[[Category: Severe acute respiratory syndrome-related coronavirus]]
-	~~[[Category: Wang, A H]]~~	+	[[Category: Lee CC]]
-	~~[[Category: Atp~~-~~binding~~]]	+	[[Category: Wang AH]]
-	[[Category: ~~Complex~~]]	+
-	[[Category: ~~Cytoplasm]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Ribosomal frameshift]]~~	+
-	~~[[Category: Rna replication]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rna-directed rna polymerase]]~~	+
-	~~[[Category: Thiol protease]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 12:00, 29 July 2020

OCA — Wed, 29 Jul 2020 12:00:32 GMT

←Older revision		Revision as of 12:00, 29 July 2020
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	==Complex structure of SARS-CoV 3C-like protease with EPDTC==		==Complex structure of SARS-CoV 3C-like protease with EPDTC==
-	<StructureSection load='2z9j' size='340' side='right' caption='[[2z9j]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='2z9j' size='340' side='right'caption='[[2z9j]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9g\|2z9g]], [[2z9k\|2z9k]], [[2z9l\|2z9l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9g\|2z9g]], [[2z9k\|2z9k]], [[2z9l\|2z9l]]</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=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [http://pdbe.org/2z9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [http://www.ebi.ac.uk/pdbsum/2z9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9j ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [http://pdbe.org/2z9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [http://www.ebi.ac.uk/pdbsum/2z9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]		*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]
-	*[[Virus ~~protease~~\|Virus ~~protease~~]]	+	*[[Virus proteases 3D strutures\|Virus proteases 3D strutures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Cvhsa]]		[[Category: Cvhsa]]
		+	[[Category: Large Structures]]
	[[Category: Lee, C C]]		[[Category: Lee, C C]]
	[[Category: Wang, A H]]		[[Category: Wang, A H]]

OCA at 09:32, 17 October 2018

OCA — Wed, 17 Oct 2018 09:32:55 GMT

←Older revision		Revision as of 09:32, 17 October 2018
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z9/2z9j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z9/2z9j_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 32:		Line 32:
	==See Also==		==See Also==
	*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]		*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]
		+	*[[Virus protease\|Virus protease]]
	== References ==		== References ==
	<references/>		<references/>
Line 41:		Line 42:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Complex]]		[[Category: Complex]]
		+	[[Category: Cytoplasm]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
Line 58:		Line 60:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
		+	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

OCA at 23:45, 4 August 2016

OCA — Thu, 04 Aug 2016 23:45:11 GMT

←Older revision		Revision as of 23:45, 4 August 2016
Line 1:		Line 1:
		+
	==Complex structure of SARS-CoV 3C-like protease with EPDTC==		==Complex structure of SARS-CoV 3C-like protease with EPDTC==
	<StructureSection load='2z9j' size='340' side='right' caption='[[2z9j]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2z9j' size='340' side='right' caption='[[2z9j]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9g\|2z9g]], [[2z9k\|2z9k]], [[2z9l\|2z9l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9g\|2z9g]], [[2z9k\|2z9k]], [[2z9l\|2z9l]]</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=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [http://www.ebi.ac.uk/pdbsum/2z9j 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=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [http://pdbe.org/2z9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [http://www.ebi.ac.uk/pdbsum/2z9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=2z9j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	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 2z9j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sars coronavirus~~]]	+	[[Category: Cvhsa]]
	[[Category: Lee, C C]]		[[Category: Lee, C C]]
	[[Category: Wang, A H]]		[[Category: Wang, A H]]

OCA at 14:05, 25 December 2014

OCA — Thu, 25 Dec 2014 14:05:47 GMT

←Older revision		Revision as of 14:05, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9g\|2z9g]], [[2z9k\|2z9k]], [[2z9l\|2z9l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9g\|2z9g]], [[2z9k\|2z9k]], [[2z9l\|2z9l]]</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=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [http://www.ebi.ac.uk/pdbsum/2z9j 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=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [http://www.ebi.ac.uk/pdbsum/2z9j 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>
	== 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: Lee, C C.]]	+	[[Category: Lee, C C]]
-	[[Category: Wang, A H.]]	+	[[Category: Wang, A H]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Complex]]		[[Category: Complex]]

OCA at 08:13, 29 September 2014

OCA — Mon, 29 Sep 2014 08:13:40 GMT

←Older revision		Revision as of 08:13, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2z9j.~~png~~\|~~left~~\|200px]]	+	==Complex structure of SARS-CoV 3C-like protease with EPDTC==
		+	<StructureSection load='2z9j' size='340' side='right' caption='[[2z9j]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z9j]] 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=2Z9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DTZ:ZINC(II)HYDROGENSULFIDE'>DTZ</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9g\|2z9g]], [[2z9k\|2z9k]], [[2z9l\|2z9l]]</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=2z9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9j RCSB], [http://www.ebi.ac.uk/pdbsum/2z9j PDBsum]</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/z9/2z9j_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 ==
		+	Five active metal-conjugated inhibitors (PMA, TDT, EPDTC, JMF1586 and JMF1600) bound with the 3C-like protease of severe acute respiratory syndrome (SARS)-associated coronavirus were analyzed crystallographically. The complex structures reveal two major inhibition modes: Hg(2+)-PMA is coordinated to C(44), M(49) and Y(54) with a square planar geometry at the S3 pocket, whereas each Zn(2+) of the four zinc-inhibitors is tetrahedrally coordinated to the H(41)-C(145) catalytic dyad. For anti-SARS drug design, this Zn(2+)-centered coordination pattern would serve as a starting platform for inhibitor optimization.

-	~~{{STRUCTURE_2z9j\| PDB=2z9j \| SCENE= }}~~	+	Structural basis of mercury- and zinc-conjugated complexes as SARS-CoV 3C-like protease inhibitors.,Lee CC, Kuo CJ, Hsu MF, Liang PH, Fang JM, Shie JJ, Wang AH FEBS Lett. 2007 Nov 27;581(28):5454-8. Epub 2007 Nov 5. PMID:17981158<ref>PMID:17981158</ref>

-	~~===Complex structure~~ of ~~SARS-CoV 3C-like protease with EPDTC===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17981158}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2z9j]] 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=2Z9J OCA].~~	+

	==See Also==		==See Also==
	*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]		*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017981158<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Sars coronavirus]]		[[Category: Sars coronavirus]]
	[[Category: Lee, C C.]]		[[Category: Lee, C C.]]

OCA at 17:36, 20 October 2012

OCA — Sat, 20 Oct 2012 17:36:40 GMT

←Older revision		Revision as of 17:36, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2z9j]] is a 2 chain structure ~~of [[SARS Coronavirus Main Proteinase]]~~ 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=2Z9J OCA].	+	[[2z9j]] 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=2Z9J OCA].

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

OCA: Protected "2z9j" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 01:28:35 GMT

Protected "2z9j" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:28, 27 July 2012

OCA at 01:28, 27 July 2012

OCA — Fri, 27 Jul 2012 01:28:33 GMT

←Older revision		Revision as of 01:28, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z9j.png\|left\|200px]]		[[Image:2z9j.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z9j", 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_2z9j\| PDB=2z9j \| SCENE= }}		{{STRUCTURE_2z9j\| PDB=2z9j \| SCENE= }}

	===Complex structure of SARS-CoV 3C-like protease with EPDTC===		===Complex structure of SARS-CoV 3C-like protease with EPDTC===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17981158}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17981158 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17981158}}		{{ABSTRACT_PUBMED_17981158}}

	==About this Structure==		==About this Structure==
-	~~2Z9J~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=2Z9J OCA].	+	[[2z9j]] is a 2 chain structure of [[SARS Coronavirus Main Proteinase]] 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=2Z9J OCA].
		+
		+	==See Also==
		+	*[[SARS Coronavirus Main Proteinase\|SARS Coronavirus Main Proteinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17981158~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017981158</ref><references group="xtra"/>
	[[Category: Sars coronavirus]]		[[Category: Sars coronavirus]]
	[[Category: Lee, C C.]]		[[Category: Lee, C C.]]
Line 29:		Line 20:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Complex]]		[[Category: Complex]]
-	[[Category: Cytoplasm]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
Line 47:		Line 37:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
-	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:13:37 2009''

OCA at 16:13, 17 February 2009

OCA — Tue, 17 Feb 2009 16:13:38 GMT

←Older revision		Revision as of 16:13, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z9J is a ~~[[Single protein]]~~ structure of ~~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=2Z9J OCA].	+	2Z9J is a 2 chains structure of sequences 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=2Z9J OCA].

	==Reference==		==Reference==
-	Structural basis of mercury- and zinc-conjugated complexes as SARS-CoV 3C-like protease inhibitors., Lee CC, Kuo CJ, Hsu MF, Liang PH, Fang JM, Shie JJ, Wang AH, FEBS Lett. 2007 Nov 27;581(28):5454-8. Epub 2007 Nov 5. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17981158 17981158]~~	+	<ref group="xtra">PMID:17981158</ref><references group="xtra"/>
	[[Category: Sars coronavirus]]		[[Category: Sars coronavirus]]
-	[[Category: Single protein]]
	[[Category: Lee, C C.]]		[[Category: Lee, C C.]]
	[[Category: Wang, A H.]]		[[Category: Wang, A H.]]
Line 51:		Line 50:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 01~~:59:~~49 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:13:37 2009''