4r3d: Difference between revisions

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 <StructureSection load='4r3d' size='340' side='right'caption='[[4r3d]], [[Resolution|resolution]] 2.82&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4r3d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Betacoronavirus_england_1 Betacoronavirus england 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R3D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4r3d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Betacoronavirus_England_1 Betacoronavirus England 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R3D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4r3g|4r3g]]</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=4r3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r3d OCA], [https://pdbe.org/4r3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r3d RCSB], [https://www.ebi.ac.uk/pdbsum/4r3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r3d ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">1a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1263720 Betacoronavirus England 1])</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=4r3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r3d OCA], [http://pdbe.org/4r3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r3d RCSB], [http://www.ebi.ac.uk/pdbsum/4r3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r3d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/R1A_CVEMC R1A_CVEMC]] 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 (By similarity).  The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites.  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) (By similarity).  The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction.  Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.  Nsp9 is a ssRNA-binding protein.  Non-structural protein 1: binds to the 40S ribosomal subunit and inhibits host translation. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response (By similarity).
+[https://www.uniprot.org/uniprot/R1A_MERS1 R1A_MERS1] 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.[UniProtKB:P0C6X7]  Promotes the degradation of host mRNAs by inducing an endonucleolytic RNA cleavage in template mRNAs, and inhibits of host mRNA translation, a function that is separable from its RNA cleavage activity. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.<ref>PMID:26311885</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.[UniProtKB:P0C6X7]  Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates, together with nsp4, in the assembly of virally induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B. signaling.[UniProtKB:P0C6X7]<ref>PMID:25142582</ref>   Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.[UniProtKB:P0C6X7]  Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Also able to bind an ADP-ribose-1''-phosphate (ADRP).[UniProtKB:P0C6X7][PROSITE-ProRule:PRU00772]  Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.[UniProtKB:P0C6X7]  Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7]  Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7]  May participate in viral replication by acting as a ssRNA-binding protein.[UniProtKB:P0C6X7]  Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.[UniProtKB:P0C6X7]
 ==See Also==
-*[[SARS Coronavirus Main Proteinase|SARS Coronavirus Main Proteinase]]
+*[[Virus protease 3D structures|Virus protease 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Betacoronavirus england 1]]
+[[Category: Betacoronavirus England 1]]
 [[Category: Large Structures]]
-[[Category: Kong, L Y]]
+[[Category: Kong LY]]
-[[Category: Lou, Z Y]]
+[[Category: Lou ZY]]
-[[Category: Ming, Z H]]
+[[Category: Ming ZH]]
-[[Category: Rao, Z H]]
+[[Category: Rao ZH]]
-[[Category: Shaw, N]]
+[[Category: Shaw N]]
-[[Category: Sun, Y N]]
+[[Category: Sun YN]]
-[[Category: Wang, Q]]
+[[Category: Wang Q]]
-[[Category: Yan, L M]]
+[[Category: Yan LM]]
-[[Category: Beta strand]]
-[[Category: Hydrolase]]
-[[Category: Zinc finger]]