5c94 - Revision history

OCA at 09:08, 20 March 2024

OCA — Wed, 20 Mar 2024 09:08:32 GMT

←Older revision		Revision as of 09:08, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_M41) Avian infectious bronchitis virus (strain M41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C94 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_M41) Avian infectious bronchitis virus (strain M41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C94 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.438Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [https://pdbe.org/5c94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [https://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [https://pdbe.org/5c94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [https://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM] 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. The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (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. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.		[https://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM] 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. The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (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. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The potential for infection by coronaviruses (CoVs) has become a serious concern with the recent emergence of Middle East respiratory syndrome and severe acute respiratory syndrome (SARS) in the human population. CoVs encode two large polyproteins, which are then processed into 15-16 nonstructural proteins (nsps) that make significant contributions to viral replication and transcription by assembling the RNA replicase complex. Among them, nsp9 plays an essential role in viral replication by forming a homodimer that binds single-stranded RNA. Thus, disrupting nsp9 dimerization is a potential anti-CoV therapy. However, different nsp9 dimer forms have been reported for alpha- and beta-CoVs, and no structural information is available for gamma-CoVs. Here we determined the crystal structure of nsp9 from the avian infectious bronchitis virus (IBV), a representative gamma-CoV that affects the economy of the poultry industry because it can infect domestic fowl. IBV nsp9 forms a homodimer via interactions across a hydrophobic interface, which consists of two parallel alpha helices near the carboxy terminus of the protein. The IBV nsp9 dimer resembles that of SARS-CoV nsp9, indicating that this type of dimerization is conserved among all CoVs. This makes disruption of the dimeric interface an excellent strategy for developing anti-CoV therapies. To facilitate this effort, we characterized the roles of six conserved residues on this interface using site-directed mutagenesis and a multitude of biochemical and biophysical methods. We found that three residues are critical for nsp9 dimerization and its abitlity to bind RNA.
-
-	Structural basis for dimerization and RNA binding of avian infectious bronchitis virus nsp9.,Hu T, Chen C, Li H, Dou Y, Zhou M, Lu D, Zong Q, Li Y, Yang C, Zhong Z, Singh N, Hu H, Zhang R, Yang H, Su D Protein Sci. 2017 May;26(5):1037-1048. doi: 10.1002/pro.3150. Epub 2017 Apr 20. PMID:28257598<ref>PMID:28257598</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5c94" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:24, 7 June 2023

OCA — Wed, 07 Jun 2023 06:24:57 GMT

←Older revision		Revision as of 06:24, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5c94' size='340' side='right'caption='[[5c94]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='5c94' size='340' side='right'caption='[[5c94]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(~~strain_m41~~) Avian infectious bronchitis virus (strain ~~m41~~)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5C94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_M41) Avian infectious bronchitis virus (strain M41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C94 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11127 Avian infectious bronchitis virus (strain M41)])</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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [https://pdbe.org/5c94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [https://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [~~http~~://pdbe.org/5c94 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM]] 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. The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (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. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.	+	[https://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM] 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. The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (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. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, C]]	+	[[Category: Chen C]]
-	[[Category: Dou, Y]]	+	[[Category: Dou Y]]
-	[[Category: Su, D]]	+	[[Category: Su D]]
-	[[Category: Yang, H]]	+	[[Category: Yang H]]
-	~~[[Category: Coronaviurs rna replicase]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nsp]]~~	+
-	~~[[Category: Rna binding protein~~]]	+

OCA at 06:44, 25 June 2020

OCA — Thu, 25 Jun 2020 06:44:49 GMT

←Older revision		Revision as of 06:44, 25 June 2020
Line 3:		Line 3:
	<StructureSection load='5c94' size='340' side='right'caption='[[5c94]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='5c94' size='340' side='right'caption='[[5c94]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_m41) Avian infectious bronchitis virus (strain m41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5C94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_m41) Avian infectious bronchitis virus (strain m41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5C94 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11127 Avian infectious bronchitis virus (strain M41)])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11127 Avian infectious bronchitis virus (strain M41)])</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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [http://pdbe.org/5c94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [http://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [http://pdbe.org/5c94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [http://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM]] 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. The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (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. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.		[[http://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM]] 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. The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (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. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The potential for infection by coronaviruses (CoVs) has become a serious concern with the recent emergence of Middle East respiratory syndrome and severe acute respiratory syndrome (SARS) in the human population. CoVs encode two large polyproteins, which are then processed into 15-16 nonstructural proteins (nsps) that make significant contributions to viral replication and transcription by assembling the RNA replicase complex. Among them, nsp9 plays an essential role in viral replication by forming a homodimer that binds single-stranded RNA. Thus, disrupting nsp9 dimerization is a potential anti-CoV therapy. However, different nsp9 dimer forms have been reported for alpha- and beta-CoVs, and no structural information is available for gamma-CoVs. Here we determined the crystal structure of nsp9 from the avian infectious bronchitis virus (IBV), a representative gamma-CoV that affects the economy of the poultry industry because it can infect domestic fowl. IBV nsp9 forms a homodimer via interactions across a hydrophobic interface, which consists of two parallel alpha helices near the carboxy terminus of the protein. The IBV nsp9 dimer resembles that of SARS-CoV nsp9, indicating that this type of dimerization is conserved among all CoVs. This makes disruption of the dimeric interface an excellent strategy for developing anti-CoV therapies. To facilitate this effort, we characterized the roles of six conserved residues on this interface using site-directed mutagenesis and a multitude of biochemical and biophysical methods. We found that three residues are critical for nsp9 dimerization and its abitlity to bind RNA.
		+
		+	Structural basis for dimerization and RNA binding of avian infectious bronchitis virus nsp9.,Hu T, Chen C, Li H, Dou Y, Zhou M, Lu D, Zong Q, Li Y, Yang C, Zhong Z, Singh N, Hu H, Zhang R, Yang H, Su D Protein Sci. 2017 May;26(5):1037-1048. doi: 10.1002/pro.3150. Epub 2017 Apr 20. PMID:28257598<ref>PMID:28257598</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5c94" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:28, 27 March 2020

OCA — Fri, 27 Mar 2020 11:28:39 GMT

←Older revision		Revision as of 11:28, 27 March 2020
Line 1:		Line 1:

	==Infectious bronchitis virus nsp9==		==Infectious bronchitis virus nsp9==
-	<StructureSection load='5c94' size='340' side='right' caption='[[5c94]], [[Resolution\|resolution]] 2.44Å' scene=''>	+	<StructureSection load='5c94' size='340' side='right'caption='[[5c94]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_m41) Avian infectious bronchitis virus (strain m41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C94 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11127 Avian infectious bronchitis virus (strain M41)])</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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [http://pdbe.org/5c94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [http://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [http://pdbe.org/5c94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [http://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chen, C]]		[[Category: Chen, C]]
	[[Category: Dou, Y]]		[[Category: Dou, Y]]

OCA at 10:19, 13 July 2016

OCA — Wed, 13 Jul 2016 10:19:56 GMT

←Older revision		Revision as of 10:19, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5c94 is ~~ON HOLD until Jun 26 2017~~	+	==Infectious bronchitis virus nsp9==
-		+	<StructureSection load='5c94' size='340' side='right' caption='[[5c94]], [[Resolution\|resolution]] 2.44Å' scene=''>
-	~~Authors~~: ~~Chen~~, C., ~~Dou~~, Y., ~~Yang~~, H., Su, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C94 FirstGlance]. <br>
-	~~Description~~: ~~Infectious bronchitis virus nsp9~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [http://pdbe.org/5c94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [http://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM]] 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. The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (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. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, C]]
		+	[[Category: Dou, Y]]
	[[Category: Su, D]]		[[Category: Su, D]]
	[[Category: Yang, H]]		[[Category: Yang, H]]
-	[[Category: ~~Dou, Y~~]]	+	[[Category: Coronaviurs rna replicase]]
-	[[Category: ~~Chen, C~~]]	+	[[Category: Homodimer]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nsp]]
		+	[[Category: Rna binding protein]]

OCA at 10:24, 16 December 2015

OCA — Wed, 16 Dec 2015 10:24:15 GMT

←Older revision		Revision as of 10:24, 16 December 2015
Line 7:		Line 7:
	Description: Infectious bronchitis virus nsp9		Description: Infectious bronchitis virus nsp9
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Su, D]]
	[[Category: Yang, H]]		[[Category: Yang, H]]
	[[Category: Dou, Y]]		[[Category: Dou, Y]]
-	[[Category: Su, D]]
	[[Category: Chen, C]]		[[Category: Chen, C]]

OCA at 09:02, 9 September 2015

OCA — Wed, 09 Sep 2015 09:02:17 GMT

←Older revision		Revision as of 09:02, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5c94 is ON HOLD	+	The entry 5c94 is ON HOLD until Jun 26 2017

	Authors: Chen, C., Dou, Y., Yang, H., Su, D.		Authors: Chen, C., Dou, Y., Yang, H., Su, D.

OCA at 13:50, 8 July 2015

OCA — Wed, 08 Jul 2015 13:50:30 GMT

←Older revision		Revision as of 13:50, 8 July 2015
Line 3:		Line 3:
	The entry 5c94 is ON HOLD		The entry 5c94 is ON HOLD

-	Authors: ~~Cheng~~ Chen, ~~Yanshu~~ Dou, ~~Haitao~~ Yang, ~~Dan~~ Su	+	Authors: Chen, C., Dou, Y., Yang, H., Su, D.

-	Description: ~~infectious~~ bronchitis virus nsp9	+	Description: Infectious bronchitis virus nsp9
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Cheng Chen~~, ~~Yanshu~~ Dou, ~~Haitao Yang, Dan~~ Su]]	+	[[Category: Yang, H]]
		+	[[Category: Dou, Y]]
		+	[[Category: Su, D]]
		+	[[Category: Chen, C]]

OCA: Protected "5c94" [edit=sysop:move=sysop]

OCA — Wed, 01 Jul 2015 11:20:24 GMT

Protected "5c94" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:20, 1 July 2015

OCA: New page: '''Unreleased structure''' The entry 5c94 is ON HOLD Authors: Cheng Chen, Yanshu Dou, Haitao Yang, Dan Su Description: infectious bronchitis virus nsp9 [[Category: Unreleased Structure...

OCA — Wed, 01 Jul 2015 11:20:22 GMT

New page: '''Unreleased structure''' The entry 5c94 is ON HOLD Authors: Cheng Chen, Yanshu Dou, Haitao Yang, Dan Su Description: infectious bronchitis virus nsp9 [[Category: Unreleased Structure...

New page

'''Unreleased structure'''

The entry 5c94 is ON HOLD

Authors: Cheng Chen, Yanshu Dou, Haitao Yang, Dan Su

Description: infectious bronchitis virus nsp9
[[Category: Unreleased Structures]]
[[Category: Cheng Chen, Yanshu Dou, Haitao Yang, Dan Su]]