1nd3 - Revision history

OCA at 07:55, 14 February 2024

OCA — Wed, 14 Feb 2024 07:55:30 GMT

←Older revision		Revision as of 07:55, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1nd3' size='340' side='right'caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1nd3' size='340' side='right'caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human_rhinovirus_16 Human rhinovirus 16~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_A16 Rhinovirus A16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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]] 2.8Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [https://pdbe.org/1nd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd3 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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [https://pdbe.org/1nd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_HRV16 POLG_HRV16]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).	+	[https://www.uniprot.org/uniprot/POLG_HRV16 POLG_HRV16] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1nd3 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=1nd3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of human rhinovirus 16 (HRV16) and HRV14 are incubated with pleconaril, drug occupancy in the binding pocket is lower than when pleconaril is introduced during assembly prior to crystallization. This effect is far more marked in HRV16 than in HRV14 and is more marked with pleconaril than with other compounds. These observations are consistent with virus yield inhibition studies and radiolabeled drug binding studies showing that the antiviral effect of pleconaril against HRV16 is greater on the infectivity of progeny virions than the parent input viruses. These data suggest that drug integration into the binding pocket during assembly, or at some other late stage in virus replication, may contribute to the antiviral activity of capsid binding compounds.
-
-	Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds.,Zhang Y, Simpson AA, Ledford RM, Bator CM, Chakravarty S, Skochko GA, Demenczuk TM, Watanyar A, Pevear DC, Rossmann MG J Virol. 2004 Oct;78(20):11061-9. PMID:15452226<ref>PMID:15452226</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nd3" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human rhinovirus 16]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bator~~, C M~~]]	+	[[Category: Rhinovirus A16]]
-	[[Category: Chakravarty, S]]	+	[[Category: Bator CM]]
-	[[Category: Diana, G]]	+	[[Category: Chakravarty S]]
-	[[Category: Pevear~~, D C~~]]	+	[[Category: Diana G]]
-	[[Category: Rossmann~~, M G~~]]	+	[[Category: Pevear DC]]
-	[[Category: Simpson~~, A A~~]]	+	[[Category: Rossmann MG]]
-	[[Category: Skochko~~, G A~~]]	+	[[Category: Simpson AA]]
-	[[Category: Tull~~, T M~~]]	+	[[Category: Skochko GA]]
-	[[Category: Zhang, Y]]	+	[[Category: Tull TM]]
-	~~[[Category: Hrv16]]~~	+	[[Category: Zhang Y]]
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Piconaviridae]]~~	+
-	~~[[Category: Pleconaril]]~~	+
-	~~[[Category: Rhinovirus]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 07:01, 25 August 2021

OCA — Wed, 25 Aug 2021 07:01:19 GMT

←Older revision		Revision as of 07:01, 25 August 2021
Line 3:		Line 3:
	<StructureSection load='1nd3' size='340' side='right'caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1nd3' size='340' side='right'caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human_rhinovirus_16 Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rhinovirus_16 Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [~~http~~://pdbe.org/1nd3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nd3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd3 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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [https://pdbe.org/1nd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLG_HRV16 POLG_HRV16]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).	+	[[https://www.uniprot.org/uniprot/POLG_HRV16 POLG_HRV16]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 18:15, 20 November 2019

OCA — Wed, 20 Nov 2019 18:15:36 GMT

←Older revision		Revision as of 18:15, 20 November 2019
Line 1:		Line 1:

	==The structure of HRV16, when complexed with pleconaril, an antiviral compound==		==The structure of HRV16, when complexed with pleconaril, an antiviral compound==
-	<StructureSection load='1nd3' size='340' side='right' caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1nd3' size='340' side='right'caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_16 Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_16 Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Human rhinovirus 16]]		[[Category: Human rhinovirus 16]]
		+	[[Category: Large Structures]]
	[[Category: Bator, C M]]		[[Category: Bator, C M]]
	[[Category: Chakravarty, S]]		[[Category: Chakravarty, S]]

OCA at 07:04, 7 February 2018

OCA — Wed, 07 Feb 2018 07:04:38 GMT

←Older revision		Revision as of 07:04, 7 February 2018
Line 1:		Line 1:
		+
	==The structure of HRV16, when complexed with pleconaril, an antiviral compound==		==The structure of HRV16, when complexed with pleconaril, an antiviral compound==
	<StructureSection load='1nd3' size='340' side='right' caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1nd3' size='340' side='right' caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Hrv-16 Hrv-~~16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_16 Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://pdbe.org/1nd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://pdbe.org/1nd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1nd3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1nd3_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 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hrv-~~16]]	+	[[Category: Human rhinovirus 16]]
	[[Category: Bator, C M]]		[[Category: Bator, C M]]
	[[Category: Chakravarty, S]]		[[Category: Chakravarty, S]]

OCA at 01:55, 7 February 2016

OCA — Sun, 07 Feb 2016 01:55:49 GMT

←Older revision		Revision as of 01:55, 7 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nd3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:34, 9 September 2015

OCA — Wed, 09 Sep 2015 20:34:42 GMT

←Older revision		Revision as of 20:34, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1nd3' size='340' side='right' caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1nd3' size='340' side='right' caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_rhinovirus_a16 Human rhinovirus a16~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-16 Hrv-16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://pdbe.org/1nd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1nd3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human rhinovirus a16~~]]	+	[[Category: Hrv-16]]
	[[Category: Bator, C M]]		[[Category: Bator, C M]]
	[[Category: Chakravarty, S]]		[[Category: Chakravarty, S]]

OCA at 06:51, 24 December 2014

OCA — Wed, 24 Dec 2014 06:51:28 GMT

←Older revision		Revision as of 06:51, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</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=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLG_HRV16 POLG_HRV16]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Human rhinovirus a16]]		[[Category: Human rhinovirus a16]]
-	[[Category: Bator, C M.]]	+	[[Category: Bator, C M]]
-	[[Category: Chakravarty, S.]]	+	[[Category: Chakravarty, S]]
-	[[Category: Diana, G.]]	+	[[Category: Diana, G]]
-	[[Category: Pevear, D C.]]	+	[[Category: Pevear, D C]]
-	[[Category: Rossmann, M G.]]	+	[[Category: Rossmann, M G]]
-	[[Category: Simpson, A A.]]	+	[[Category: Simpson, A A]]
-	[[Category: Skochko, G A.]]	+	[[Category: Skochko, G A]]
-	[[Category: Tull, T M.]]	+	[[Category: Tull, T M]]
-	[[Category: Zhang, Y.]]	+	[[Category: Zhang, Y]]
	[[Category: Hrv16]]		[[Category: Hrv16]]
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]

OCA at 08:22, 3 October 2014

OCA — Fri, 03 Oct 2014 08:22:54 GMT

←Older revision		Revision as of 08:22, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1nd3.~~png~~\|~~left~~\|200px]]	+	==The structure of HRV16, when complexed with pleconaril, an antiviral compound==
		+	<StructureSection load='1nd3' size='340' side='right' caption='[[1nd3]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1na1\|1na1]], [[1ncq\|1ncq]], [[1ncr\|1ncr]], [[1nd2\|1nd2]]</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=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 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/nd/1nd3_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 ==
		+	Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of human rhinovirus 16 (HRV16) and HRV14 are incubated with pleconaril, drug occupancy in the binding pocket is lower than when pleconaril is introduced during assembly prior to crystallization. This effect is far more marked in HRV16 than in HRV14 and is more marked with pleconaril than with other compounds. These observations are consistent with virus yield inhibition studies and radiolabeled drug binding studies showing that the antiviral effect of pleconaril against HRV16 is greater on the infectivity of progeny virions than the parent input viruses. These data suggest that drug integration into the binding pocket during assembly, or at some other late stage in virus replication, may contribute to the antiviral activity of capsid binding compounds.

-	~~{{STRUCTURE_1nd3\| PDB=1nd3 \| SCENE= }}~~	+	Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds.,Zhang Y, Simpson AA, Ledford RM, Bator CM, Chakravarty S, Skochko GA, Demenczuk TM, Watanyar A, Pevear DC, Rossmann MG J Virol. 2004 Oct;78(20):11061-9. PMID:15452226<ref>PMID:15452226</ref>

-	~~===The structure of HRV16~~, ~~when complexed with pleconaril, an antiviral compound===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15452226}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1nd3]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015452226<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Human rhinovirus a16]]		[[Category: Human rhinovirus a16]]
	[[Category: Bator, C M.]]		[[Category: Bator, C M.]]

OCA: Protected "1nd3" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 19:40:20 GMT

Protected "1nd3" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:40, 5 December 2012

OCA at 19:40, 5 December 2012

OCA — Wed, 05 Dec 2012 19:40:17 GMT

←Older revision		Revision as of 19:40, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1nd3.png\|left\|200px]]		[[Image:1nd3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nd3", 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_1nd3\| PDB=1nd3 \| SCENE= }}		{{STRUCTURE_1nd3\| PDB=1nd3 \| SCENE= }}

	===The structure of HRV16, when complexed with pleconaril, an antiviral compound===		===The structure of HRV16, when complexed with pleconaril, an antiviral compound===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15452226}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15452226 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15452226}}		{{ABSTRACT_PUBMED_15452226}}

	==About this Structure==		==About this Structure==
-	~~1ND3~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Human_rhinovirus_16~~ Human rhinovirus 16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA].	+	[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15452226~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015452226</ref><references group="xtra"/>
-	[[Category: Human rhinovirus 16]]	+	[[Category: Human rhinovirus a16]]
	[[Category: Bator, C M.]]		[[Category: Bator, C M.]]
	[[Category: Chakravarty, S.]]		[[Category: Chakravarty, S.]]
Line 39:		Line 27:
	[[Category: Pleconaril]]		[[Category: Pleconaril]]
	[[Category: Rhinovirus]]		[[Category: Rhinovirus]]
-		+	[[Category: Virus]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 10:02:05 2009''~~	+