2hwd - Revision history

OCA at 19:03, 29 May 2024

OCA — Wed, 29 May 2024 19:03:22 GMT

←Older revision		Revision as of 19:03, 29 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rhinovirus_1A Human rhinovirus 1A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HWD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rhinovirus_1A Human rhinovirus 1A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</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]] 3.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [https://pdbe.org/2hwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [https://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd 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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [https://pdbe.org/2hwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [https://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd 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 06:52, 8 February 2023

OCA — Wed, 08 Feb 2023 06:52:15 GMT

←Older revision		Revision as of 06:52, 8 February 2023
Line 3:		Line 3:
	<StructureSection load='2hwd' size='340' side='right'caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='2hwd' size='340' side='right'caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hrv-1a Hrv-1a~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rhinovirus_1A Human rhinovirus 1A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [https://pdbe.org/2hwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [https://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd 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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [https://pdbe.org/2hwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [https://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_HRV1A POLG_HRV1A]] Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor VLDLR to provide virion attachment to target cell. This attachment induces virion internalization through a cell-type specific entry mechanism. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity). Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factors EIF4G1, in order to shut off the capped cellular mRNA transcription. Protease 2A also degrades host nucleoporins NUP62, NUP98 and NUP153 thereby blocking the nucleo-cytoplasmic trafficking, in particular the export of cellular mRNAs. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (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: 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 cooperatively to the protease. Cleaves Nup153, Nup214, and Nup358 thereby blocking the nucleo-cytoplasmic trafficking. Contributes to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown (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_HRV1A POLG_HRV1A] Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor VLDLR to provide virion attachment to target cell. This attachment induces virion internalization through a cell-type specific entry mechanism. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity). Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factors EIF4G1, in order to shut off the capped cellular mRNA transcription. Protease 2A also degrades host nucleoporins NUP62, NUP98 and NUP153 thereby blocking the nucleo-cytoplasmic trafficking, in particular the export of cellular mRNAs. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (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: 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 cooperatively to the protease. Cleaves Nup153, Nup214, and Nup358 thereby blocking the nucleo-cytoplasmic trafficking. Contributes to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown (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 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hrv-1a~~]]	+	[[Category: Human rhinovirus 1A]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, K H~~]]	+	[[Category: Kim KH]]
-	[[Category: Rossmann~~, M G]]~~	+	[[Category: Rossmann MG]]
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Rhinovirus coat protein]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 10:23, 12 January 2022

OCA — Wed, 12 Jan 2022 10:23:13 GMT

←Older revision		Revision as of 10:23, 12 January 2022
Line 3:		Line 3:
	<StructureSection load='2hwd' size='340' side='right'caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='2hwd' size='340' side='right'caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Hrv-1a Hrv-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2HWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hrv-1a Hrv-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [~~http~~://pdbe.org/2hwd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd 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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [https://pdbe.org/2hwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [https://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLG_HRV1A POLG_HRV1A]] Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor VLDLR to provide virion attachment to target cell. This attachment induces virion internalization through a cell-type specific entry mechanism. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity). Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factors EIF4G1, in order to shut off the capped cellular mRNA transcription. Protease 2A also degrades host nucleoporins NUP62, NUP98 and NUP153 thereby blocking the nucleo-cytoplasmic trafficking, in particular the export of cellular mRNAs. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (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: 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 cooperatively to the protease. Cleaves Nup153, Nup214, and Nup358 thereby blocking the nucleo-cytoplasmic trafficking. Contributes to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown (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_HRV1A POLG_HRV1A]] Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor VLDLR to provide virion attachment to target cell. This attachment induces virion internalization through a cell-type specific entry mechanism. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity). Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factors EIF4G1, in order to shut off the capped cellular mRNA transcription. Protease 2A also degrades host nucleoporins NUP62, NUP98 and NUP153 thereby blocking the nucleo-cytoplasmic trafficking, in particular the export of cellular mRNAs. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (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: 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 cooperatively to the protease. Cleaves Nup153, Nup214, and Nup358 thereby blocking the nucleo-cytoplasmic trafficking. Contributes to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown (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 07:40, 8 April 2020

OCA — Wed, 08 Apr 2020 07:40:02 GMT

←Older revision		Revision as of 07:40, 8 April 2020
Line 1:		Line 1:

	==A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A==		==A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A==
-	<StructureSection load='2hwd' size='340' side='right' caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<StructureSection load='2hwd' size='340' side='right'caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-1a Hrv-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-1a Hrv-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://pdbe.org/2hwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd 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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://pdbe.org/2hwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Hrv-1a]]		[[Category: Hrv-1a]]
		+	[[Category: Large Structures]]
	[[Category: Kim, K H]]		[[Category: Kim, K H]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]

OCA at 08:33, 4 July 2018

OCA — Wed, 04 Jul 2018 08:33:03 GMT

←Older revision		Revision as of 08:33, 4 July 2018
Line 1:		Line 1:
		+
	==A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A==		==A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A==
	<StructureSection load='2hwd' size='340' side='right' caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='2hwd' size='340' side='right' caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-1a Hrv-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HWD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-1a Hrv-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://pdbe.org/2hwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd 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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://pdbe.org/2hwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hwd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hw/2hwd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hw/2hwd_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 21:34, 7 February 2016

OCA — Sun, 07 Feb 2016 21:34:04 GMT

←Older revision		Revision as of 21:34, 7 February 2016
Line 16:		Line 16:
	<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=2hwd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:09, 10 September 2015

OCA — Thu, 10 Sep 2015 05:09:33 GMT

←Older revision		Revision as of 05:09, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2hwd' size='340' side='right' caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='2hwd' size='340' side='right' caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_rhinovirus_1a Human rhinovirus~~ 1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-1a Hrv-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd 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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://pdbe.org/2hwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 2hwd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Human rhinovirus\|Human rhinovirus]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human rhinovirus~~ 1a]]	+	[[Category: Hrv-1a]]
	[[Category: Kim, K H]]		[[Category: Kim, K H]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]

OCA at 18:23, 24 December 2014

OCA — Wed, 24 Dec 2014 18:23:13 GMT

←Older revision		Revision as of 18:23, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_1a Human rhinovirus 1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HWD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_1a Human rhinovirus 1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene></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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd 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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLG_HRV1A POLG_HRV1A]] Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor VLDLR to provide virion attachment to target cell. This attachment induces virion internalization through a cell-type specific entry mechanism. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity). Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factors EIF4G1, in order to shut off the capped cellular mRNA transcription. Protease 2A also degrades host nucleoporins NUP62, NUP98 and NUP153 thereby blocking the nucleo-cytoplasmic trafficking, in particular the export of cellular mRNAs. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (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: 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 cooperatively to the protease. Cleaves Nup153, Nup214, and Nup358 thereby blocking the nucleo-cytoplasmic trafficking. Contributes to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown (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 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Human rhinovirus 1a]]		[[Category: Human rhinovirus 1a]]
-	[[Category: Kim, K H.]]	+	[[Category: Kim, K H]]
-	[[Category: Rossmann, M G.]]	+	[[Category: Rossmann, M G]]
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Rhinovirus coat protein]]		[[Category: Rhinovirus coat protein]]
	[[Category: Virus]]		[[Category: Virus]]

OCA at 09:06, 3 October 2014

OCA — Fri, 03 Oct 2014 09:06:53 GMT

←Older revision		Revision as of 09:06, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2hwd\| PDB=2hwd \| SCENE= }}~~	+	==A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A==
-	===A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A===	+	<StructureSection load='2hwd' size='340' side='right' caption='[[2hwd]], [[Resolution\|resolution]] 3.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_8383771}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hwd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_1a Human rhinovirus 1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HWD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W91:5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL+ISOXAZOLE'>W91</scene><br>
		+	<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=2hwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hwd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hwd RCSB], [http://www.ebi.ac.uk/pdbsum/2hwd 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/hw/2hwd_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 ==
		+	The three-dimensional structures of two human rhinovirus serotypes (HRV14 and HRV1A) are compared when complexed with various antiviral agents. Although these agents all bind into the same hydrophobic pocket, the exact viral-drug interactions differ. In the absence of drugs, the pocket is occupied by a fatty acid in HRV1A, but is empty in HRV14 except for two water molecules. The conformation of each drug is dependent upon the shape of the hydrophobic pocket. In HRV14 the major residues determining the shape of the binding site are Y1128, P1174 and M1224, corresponding to I1125, M1169 and I1220 in HRV1A. When there is no cofactor or a drug in the pocket, the entrance to the pocket is open. However, the entrance is closed when the pocket is occupied by a cofactor or a drug. There are relatively small conformational changes when the agents displace the natural cofactor in HRV1A. In contrast, there are much larger conformational changes on binding a drug in HRV14. These differences cause an inhibition of viral attachment in HRV14 but not in HRV1A. Binding of the drugs results in three additional interprotomer hydrogen bonds in HRV14 and one in HRV1A. These hydrogen bonds and a potential loss of flexibility upon efficient packing of the pocket may contribute to the inhibition of uncoating in both serotypes.

-	~~==Function==~~	+	A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A.,Kim KH, Willingmann P, Gong ZX, Kremer MJ, Chapman MS, Minor I, Oliveira MA, Rossmann MG, Andries K, Diana GD, et al. J Mol Biol. 1993 Mar 5;230(1):206-27. PMID:8383771<ref>PMID:8383771</ref>
-	~~[[http://www.uniprot.org/uniprot/POLG_HRV1A POLG_HRV1A]] Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed~~ of ~~60 copies of each capsid protein and enclosing~~ the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor VLDLR to provide virion attachment to target cell. This attachment induces virion internalization through a cell-~~type specific entry mechanism. After~~ binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in ~~the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP2: Forms, together with VP1~~ and ~~VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity)~~. ~~Protein VP3: Forms~~, ~~together with VP1 and VP2~~, ~~an icosahedral capsid (pseudo T=3)~~, ~~300 Angstroms in diameter~~, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, ~~the capsid undergoes conformational changes. VP4 is released~~, ~~VP1 N-terminus is externalized~~, ~~and together~~, ~~they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released~~, ~~the channel shrinks (By similarity). Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids~~, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity). Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factors EIF4G1, ~~in order to shut off the capped cellular mRNA transcription~~. ~~Protease 2A also degrades host nucleoporins NUP62, NUP98 and NUP153 thereby blocking the nucleo-cytoplasmic trafficking, in particular the export of cellular mRNAs~~. ~~The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response~~ (~~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~~: 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 cooperatively to the protease. Cleaves Nup153, Nup214, and Nup358 thereby blocking the nucleo-cytoplasmic trafficking. Contributes to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown (By similarity). RNA-directed RNA polymerase 3D-POL: replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2hwd]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_rhinovirus_1a Human rhinovirus 1a]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2HWD OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:008383771</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Human rhinovirus 1a]]		[[Category: Human rhinovirus 1a]]
	[[Category: Kim, K H.]]		[[Category: Kim, K H.]]

OCA at 08:39, 23 April 2014

OCA — Wed, 23 Apr 2014 08:39:18 GMT

←Older revision		Revision as of 08:39, 23 April 2014
Line 1:		Line 1:
-	[[Image:2hwd.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_2hwd", 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_2hwd\| PDB=2hwd \| SCENE= }}		{{STRUCTURE_2hwd\| PDB=2hwd \| SCENE= }}
-
	===A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A===		===A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A===
		+	{{ABSTRACT_PUBMED_8383771}}

-		+	==Function==
-	<!--	+	[[http://www.uniprot.org/uniprot/POLG_HRV1A POLG_HRV1A]] Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor VLDLR to provide virion attachment to target cell. This attachment induces virion internalization through a cell-type specific entry mechanism. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks (By similarity). Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity). Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factors EIF4G1, in order to shut off the capped cellular mRNA transcription. Protease 2A also degrades host nucleoporins NUP62, NUP98 and NUP153 thereby blocking the nucleo-cytoplasmic trafficking, in particular the export of cellular mRNAs. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (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: 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 cooperatively to the protease. Cleaves Nup153, Nup214, and Nup358 thereby blocking the nucleo-cytoplasmic trafficking. Contributes to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown (By similarity). RNA-directed RNA polymerase 3D-POL: replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_8383771}}~~, ~~adds~~ the ~~Publication Abstract to~~ the ~~page~~	+
-	(~~as it appears on PubMed at http~~:~~//www~~.~~pubmed~~.~~gov~~), ~~where 8383771~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_8383771}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:008383771</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008383771</ref><references group="xtra"/><references/>
	[[Category: Human rhinovirus 1a]]		[[Category: Human rhinovirus 1a]]
	[[Category: Kim, K H.]]		[[Category: Kim, K H.]]