4phy - Revision history

OCA at 00:44, 28 December 2023

2023-12-28T00:44:08Z

← Older revision		Revision as of 00:44, 28 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Senecavirus_A Senecavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Senecavirus_A Senecavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PHY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.1Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4phy OCA], [https://pdbe.org/4phy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4phy RCSB], [https://www.ebi.ac.uk/pdbsum/4phy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4phy 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=4phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4phy OCA], [https://pdbe.org/4phy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4phy RCSB], [https://www.ebi.ac.uk/pdbsum/4phy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4phy ProSAT]</span></td></tr>
	</table>		</table>

OCA at 13:04, 1 February 2023

2023-02-01T13:04:48Z

← Older revision		Revision as of 13:04, 1 February 2023
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	<StructureSection load='4phy' size='340' side='right'caption='[[4phy]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4phy' size='340' side='right'caption='[[4phy]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Senecavirus_A Senecavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PHY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4phy OCA], [~~http~~://pdbe.org/4phy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4phy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4phy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4phy 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=4phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4phy OCA], [https://pdbe.org/4phy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4phy RCSB], [https://www.ebi.ac.uk/pdbsum/4phy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4phy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Boerneke, M~~ A]]		[[Category: Senecavirus A]]
	[[Category: ~~Dibrov, S M~~]]		[[Category: Boerneke MA]]
	[[Category: ~~Hermann, T H~~]]		[[Category: Dibrov SM]]
	[[Category: ~~Internal ribosome entry site]]~~		[[Category: Hermann TH]]
	~~[[Category: Rna]]~~
	~~[[Category: Translation]]~~
	~~[[Category: Viral genome~~]]

OCA at 08:03, 17 April 2019

2019-04-17T08:03:21Z

← Older revision		Revision as of 08:03, 17 April 2019
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	==Functional conservation despite structural divergence in ligand-responsive RNA switches==		==Functional conservation despite structural divergence in ligand-responsive RNA switches==
	<StructureSection load='4phy' size='340' side='right' caption='[[4phy]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4phy' size='340' side='right'caption='[[4phy]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHY FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Boerneke, M A]]		[[Category: Boerneke, M A]]
	[[Category: Dibrov, S M]]		[[Category: Dibrov, S M]]

OCA at 17:08, 4 January 2017

2017-01-04T17:08:10Z

← Older revision		Revision as of 17:08, 4 January 2017
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	==Functional conservation despite structural divergence in ligand-responsive RNA switches==		==Functional conservation despite structural divergence in ligand-responsive RNA switches==
	<StructureSection load='4phy' size='340' side='right' caption='[[4phy]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4phy' size='340' side='right' caption='[[4phy]], [[Resolution\|resolution]] 3.10Å' scene=''>
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	<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4phy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4phy RCSB], [http://www.ebi.ac.uk/pdbsum/4phy 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=4phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4phy OCA], [http://pdbe.org/4phy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4phy RCSB], [http://www.ebi.ac.uk/pdbsum/4phy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4phy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4phy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:03, 18 February 2015

2015-02-18T13:03:26Z

← Older revision		Revision as of 13:03, 18 February 2015
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	'''~~Unreleased~~ structure'''		==Functional conservation despite structural divergence in ligand-responsive RNA switches==
			<StructureSection load='4phy' size='340' side='right' caption='[[4phy]], [[Resolution\|resolution]] 3.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4phy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PHY FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4phy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4phy RCSB], [http://www.ebi.ac.uk/pdbsum/4phy PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			An internal ribosome entry site (IRES) initiates protein synthesis in RNA viruses, including the hepatitis C virus (HCV). We have discovered ligand-responsive conformational switches in viral IRES elements. Modular RNA motifs of greatly distinct sequence and local secondary structure have been found to serve as functionally conserved switches involved in viral IRES-driven translation and may be captured by identical cognate ligands. The RNA motifs described here constitute a new paradigm for ligand-captured switches that differ from metabolite-sensing riboswitches with regard to their small size, as well as the intrinsic stability and structural definition of the constitutive conformational states. These viral RNA modules represent the simplest form of ligand-responsive mechanical switches in nucleic acids.

	~~The entry 4phy is ON HOLD until Paper Publication~~		Functional conservation despite structural divergence in ligand-responsive RNA switches.,Boerneke MA, Dibrov SM, Gu J, Wyles DL, Hermann T Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15952-7. doi:, 10.1073/pnas.1414678111. Epub 2014 Oct 27. PMID:25349403<ref>PMID:25349403</ref>

	~~Authors~~: Boerneke, M.A., Dibrov, S.M., Hermann, T.H.		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~Description: Functional Conservation of a Ligand Responsive Conformational Switch in RNA Viruses~~		== References ==
	[[Category: ~~Unreleased Structures~~]]		<references/>
	[[Category: ~~Boerneke, M.A~~]]		__TOC__
	[[Category: ~~Dibrov, S.M~~]]		</StructureSection>
	[[Category: ~~Hermann, T.H~~]]		[[Category: Boerneke, M A]]
			[[Category: Dibrov, S M]]
			[[Category: Hermann, T H]]
			[[Category: Internal ribosome entry site]]
			[[Category: Rna]]
			[[Category: Translation]]
			[[Category: Viral genome]]

OCA at 15:03, 24 December 2014

2014-12-24T15:03:22Z

← Older revision		Revision as of 15:03, 24 December 2014
Line 6:		Line 6:

	Description: Functional Conservation of a Ligand Responsive Conformational Switch in RNA Viruses		Description: Functional Conservation of a Ligand Responsive Conformational Switch in RNA Viruses
			[[Category: Unreleased Structures]]
			[[Category: Boerneke, M.A]]
			[[Category: Dibrov, S.M]]
			[[Category: Hermann, T.H]]

OCA at 08:04, 21 May 2014

2014-05-21T08:04:14Z

← Older revision		Revision as of 08:04, 21 May 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4phy is ON HOLD		The entry 4phy is ON HOLD until Paper Publication

	Authors: Boerneke, M.A., Dibrov, S.M., Hermann, T.H.		Authors: Boerneke, M.A., Dibrov, S.M., Hermann, T.H.

	Description: Functional Conservation of a Ligand Responsive Conformational Switch in RNA Viruses		Description: Functional Conservation of a Ligand Responsive Conformational Switch in RNA Viruses

OCA: Protected "4phy" [edit=sysop:move=sysop]

2014-05-14T07:08:34Z

Protected "4phy" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:08, 14 May 2014
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4phy is ON HOLD Authors: Boerneke, M.A., Dibrov, S.M., Hermann, T.H. Description: Functional Conservation of a Ligand Responsive Conformational Swi...

2014-05-14T07:08:33Z

New page: '''Unreleased structure''' The entry 4phy is ON HOLD Authors: Boerneke, M.A., Dibrov, S.M., Hermann, T.H. Description: Functional Conservation of a Ligand Responsive Conformational Swi...

New page

'''Unreleased structure'''

The entry 4phy is ON HOLD

Authors: Boerneke, M.A., Dibrov, S.M., Hermann, T.H.

Description: Functional Conservation of a Ligand Responsive Conformational Switch in RNA Viruses