2rs5: Difference between revisions
New page: left|200px<br /><applet load="2rs5" size="450" color="white" frame="true" align="right" spinBox="true" caption="2rs5, resolution 3.0Å" /> '''STRUCTURAL ANALYSIS O... |
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[[Image:2rs5.gif|left|200px]]<br /><applet load="2rs5" size=" | [[Image:2rs5.gif|left|200px]]<br /><applet load="2rs5" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2rs5, resolution 3.0Å" /> | caption="2rs5, resolution 3.0Å" /> | ||
'''STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES'''<br /> | '''STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES'''<br /> | ||
==Overview== | ==Overview== | ||
X-Ray diffraction data have been obtained for nine related antiviral | 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. | ||
==About this Structure== | ==About this Structure== | ||
2RS5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Human_rhinovirus_10 Human rhinovirus 10] with W56 as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | 2RS5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Human_rhinovirus_10 Human rhinovirus 10] with <scene name='pdbligand=W56:'>W56</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1RS5. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RS5 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Badger, J.]] | [[Category: Badger, J.]] | ||
[[Category: Rossmann, M | [[Category: Rossmann, M G.]] | ||
[[Category: Smith, T | [[Category: Smith, T J.]] | ||
[[Category: W56]] | [[Category: W56]] | ||
[[Category: icosahedral virus]] | [[Category: icosahedral virus]] | ||
[[Category: rhinovirus coat protein]] | [[Category: rhinovirus coat protein]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:48:44 2008'' | ||
Revision as of 19:48, 21 February 2008
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STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES
OverviewOverview
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.
About this StructureAbout this Structure
2RS5 is a Protein complex structure of sequences from Human rhinovirus 10 with as ligand. This structure supersedes the now removed PDB entry 1RS5. Full crystallographic information is available from OCA.
ReferenceReference
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
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