2rm2 - Revision history

OCA at 09:44, 22 May 2024

2024-05-22T09:44:31Z

← Older revision		Revision as of 09:44, 22 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</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]] 3Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [https://pdbe.org/2rm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [https://pdbe.org/2rm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 ProSAT]</span></td></tr>
	</table>		</table>
Line 31:		Line 32:
	==See Also==		==See Also==
	*[[Human rhinovirus\|Human rhinovirus]]		*[[Human rhinovirus\|Human rhinovirus]]
			*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:39, 18 January 2023

2023-01-18T07:39:00Z

← Older revision		Revision as of 07:39, 18 January 2023
Line 3:		Line 3:
	<StructureSection load='2rm2' size='340' side='right'caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2rm2' size='340' side='right'caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hrv-14 Hrv-14~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</div></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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [https://pdbe.org/2rm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [https://pdbe.org/2rm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/POLG_HRV14 POLG_HRV14]] 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 (By similarity). 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. 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_HRV14 POLG_HRV14] 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 (By similarity). 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. 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 36:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Hrv-14]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Badger, J~~]]		[[Category: Rhinovirus B14]]
	[[Category: ~~Rossmann, M G]]~~		[[Category: Badger J]]
	~~[[Category: Smith, T~~ J]]		[[Category: Rossmann MG]]
	[[Category: ~~Icosahedral virus~~]]		[[Category: Smith TJ]]
	[[Category: ~~Rhinovirus coat protein]]~~
	~~[[Category: Virus~~]]

OCA at 07:48, 16 March 2022

2022-03-16T07:48:19Z

← Older revision		Revision as of 07:48, 16 March 2022
Line 3:		Line 3:
	<StructureSection load='2rm2' size='340' side='right'caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2rm2' size='340' side='right'caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Hrv-14 Hrv-14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hrv-14 Hrv-14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</div></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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [~~http~~://pdbe.org/2rm2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [https://pdbe.org/2rm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/POLG_HRV14 POLG_HRV14]] 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 (By similarity). 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. 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_HRV14 POLG_HRV14]] 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 (By similarity). 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. 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 07:13, 10 June 2020

2020-06-10T07:13:04Z

← Older revision		Revision as of 07:13, 10 June 2020
Line 1:		Line 1:

	==STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES==		==STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES==
	<StructureSection load='2rm2' size='340' side='right' caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2rm2' size='340' side='right'caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-14 Hrv-14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-14 Hrv-14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://pdbe.org/2rm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://pdbe.org/2rm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Hrv-14]]		[[Category: Hrv-14]]
			[[Category: Large Structures]]
	[[Category: Badger, J]]		[[Category: Badger, J]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]

OCA at 11:22, 5 September 2018

2018-09-05T11:22:39Z

← Older revision		Revision as of 11:22, 5 September 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/rm/2rm2_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rm/2rm2_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>

OCA at 07:34, 5 August 2016

2016-08-05T07:34:53Z

← Older revision		Revision as of 07:34, 5 August 2016
Line 1:		Line 1:

	==STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES==		==STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES==
	<StructureSection load='2rm2' size='340' side='right' caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2rm2' size='340' side='right' caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_rhinovirus_b14 Human rhinovirus b14~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-14 Hrv-14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://pdbe.org/2rm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 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=2rm2 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 2rm2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human rhinovirus b14~~]]		[[Category: Hrv-14]]
	[[Category: Badger, J]]		[[Category: Badger, J]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]

OCA at 16:56, 25 December 2014

2014-12-25T16:56:28Z

← Older revision		Revision as of 16:56, 25 December 2014
Line 7:		Line 7:
	<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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/POLG_HRV14 POLG_HRV14]] 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 (By similarity). 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. 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 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Human rhinovirus b14]]		[[Category: Human rhinovirus b14]]
	[[Category: Badger, J.]]		[[Category: Badger, J]]
	[[Category: Rossmann, M G.]]		[[Category: Rossmann, M G]]
	[[Category: Smith, T J.]]		[[Category: Smith, T J]]
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Rhinovirus coat protein]]		[[Category: Rhinovirus coat protein]]
	[[Category: Virus]]		[[Category: Virus]]

OCA at 06:48, 10 October 2014

2014-10-10T06:48:07Z

← Older revision		Revision as of 06:48, 10 October 2014
Line 1:		Line 1:
	[[Image:~~2rm2~~.~~png~~\|~~left~~\|~~200px~~]]		==STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES==
			<StructureSection load='2rm2' size='340' side='right' caption='[[2rm2]], [[Resolution\|resolution]] 3.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_b14 Human rhinovirus b14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r08\|1r08]], [[1r09\|1r09]], [[2r04\|2r04]], [[2r06\|2r06]], [[2r07\|2r07]], [[2rr1\|2rr1]], [[2rs1\|2rs1]], [[2rs3\|2rs3]], [[2rs5\|2rs5]]</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=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 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/rm/2rm2_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 ==
			X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.

	~~{{STRUCTURE_2rm2\| PDB=2rm2 \| SCENE= }}~~		Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.,Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG Proteins. 1989;6(1):1-19. PMID:2558377<ref>PMID:2558377</ref>

	~~===STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_2558377}}~~		==See Also==
			*[[Human rhinovirus\|Human rhinovirus]]
	==~~About this Structure~~==		== References ==
	[[~~2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_b14~~ Human rhinovirus ~~b14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA~~].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:002558377<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Human rhinovirus b14]]		[[Category: Human rhinovirus b14]]
	[[Category: Badger, J.]]		[[Category: Badger, J.]]

OCA: Protected "2rm2" [edit=sysop:move=sysop]

2013-01-07T20:23:53Z

Protected "2rm2" [edit=sysop:move=sysop]

← Older revision	Revision as of 20:23, 7 January 2013
(No difference)

OCA at 20:23, 7 January 2013

2013-01-07T20:23:50Z

← Older revision		Revision as of 20:23, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2rm2.png\|left\|200px]]		[[Image:2rm2.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2rm2", 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_2rm2\| PDB=2rm2 \| SCENE= }}		{{STRUCTURE_2rm2\| PDB=2rm2 \| SCENE= }}

	===STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES===		===STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_2558377}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 2558377 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_2558377}}		{{ABSTRACT_PUBMED_2558377}}

	==About this Structure==		==About this Structure==
	~~2RM2~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Human_rhinovirus_14~~ Human rhinovirus 14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA].		[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_b14 Human rhinovirus b14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~2558377~~</ref><references group="xtra"/>		<ref group="xtra">PMID:002558377</ref><references group="xtra"/>
	[[Category: Human rhinovirus 14]]		[[Category: Human rhinovirus b14]]
	[[Category: Badger, J.]]		[[Category: Badger, J.]]
	[[Category: Rossmann, M G.]]		[[Category: Rossmann, M G.]]
Line 30:		Line 18:
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Rhinovirus coat protein]]		[[Category: Rhinovirus coat protein]]
			[[Category: Virus]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 22:28:02 2009''~~