4rgf - Revision history

OCA at 12:52, 1 March 2024

OCA — Fri, 01 Mar 2024 12:52:18 GMT

←Older revision		Revision as of 12:52, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RGF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.2008Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [https://pdbe.org/4rgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [https://www.ebi.ac.uk/pdbsum/4rgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rgf 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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [https://pdbe.org/4rgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [https://www.ebi.ac.uk/pdbsum/4rgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rgf ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-A crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modelled 2'-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5' bond. Both an invariant guanosine and a Mg(2+) are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site.
-
-	In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.,Ren A, Kosutic M, Rajashankar KR, Frener M, Santner T, Westhof E, Micura R, Patel DJ Nat Commun. 2014 Nov 20;5:5534. doi: 10.1038/ncomms6534. PMID:25410397<ref>PMID:25410397</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rgf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]		*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:54, 2 March 2023

OCA — Thu, 02 Mar 2023 06:54:59 GMT

←Older revision		Revision as of 06:54, 2 March 2023
Line 3:		Line 3:
	<StructureSection load='4rgf' size='340' side='right'caption='[[4rgf]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='4rgf' size='340' side='right'caption='[[4rgf]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RGF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RGF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [https://pdbe.org/4rgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [https://www.ebi.ac.uk/pdbsum/4rgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rgf ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rge\|4rge]]~~</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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [~~http~~://pdbe.org/4rgf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rgf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rgf ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 18:

	==See Also==		==See Also==
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Patel, D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Rajashankar, K R]]~~	+	[[Category: Patel D]]
-	~~[[Category: Ren, A]]~~	+	[[Category: Rajashankar KR]]
-	~~[[Category: Simanshu,~~ D]]	+	[[Category: Ren A]]
-	[[Category: ~~Cleavage~~]]	+	[[Category: Simanshu D]]
-	[[Category: ~~Pseudoknot~~]]	+
-	[[Category: ~~Rna]]~~	+
-	~~[[Category: Stem~~]]	+

OCA at 10:30, 1 May 2019

OCA — Wed, 01 May 2019 10:30:33 GMT

←Older revision		Revision as of 10:30, 1 May 2019
Line 1:		Line 1:

	==Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+==		==Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+==
-	<StructureSection load='4rgf' size='340' side='right' caption='[[4rgf]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='4rgf' size='340' side='right'caption='[[4rgf]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RGF FirstGlance]. <br>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Patel, D]]		[[Category: Patel, D]]
	[[Category: Rajashankar, K R]]		[[Category: Rajashankar, K R]]

OCA at 17:29, 18 January 2017

OCA — Wed, 18 Jan 2017 17:29:23 GMT

←Older revision		Revision as of 17:29, 18 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+==		==Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+==
	<StructureSection load='4rgf' size='340' side='right' caption='[[4rgf]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='4rgf' size='340' side='right' caption='[[4rgf]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rge\|4rge]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rge\|4rge]]</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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [http://www.ebi.ac.uk/pdbsum/4rgf 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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [http://pdbe.org/4rgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [http://www.ebi.ac.uk/pdbsum/4rgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rgf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4rgf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:25, 3 December 2014

OCA — Wed, 03 Dec 2014 09:25:03 GMT

←Older revision		Revision as of 09:25, 3 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+==
		+	<StructureSection load='4rgf' size='340' side='right' caption='[[4rgf]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RGF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rge\|4rge]]</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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [http://www.ebi.ac.uk/pdbsum/4rgf PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-A crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modelled 2'-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5' bond. Both an invariant guanosine and a Mg(2+) are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site.

-	~~The entry 4rgf is ON HOLD until Paper Publication~~	+	In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.,Ren A, Kosutic M, Rajashankar KR, Frener M, Santner T, Westhof E, Micura R, Patel DJ Nat Commun. 2014 Nov 20;5:5534. doi: 10.1038/ncomms6534. PMID:25410397<ref>PMID:25410397</ref>

-	~~Authors: Ren~~, A., Rajashankar, K.R., Simanshu, D~~., Patel, D.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Patel, D]]
		+	[[Category: Rajashankar, K R]]
		+	[[Category: Ren, A]]
		+	[[Category: Simanshu, D]]
		+	[[Category: Cleavage]]
		+	[[Category: Pseudoknot]]
		+	[[Category: Rna]]
		+	[[Category: Stem]]

OCA at 09:41, 22 October 2014

OCA — Wed, 22 Oct 2014 09:41:03 GMT

←Older revision		Revision as of 09:41, 22 October 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rgf is ON HOLD	+	The entry 4rgf is ON HOLD until Paper Publication

	Authors: Ren, A., Rajashankar, K.R., Simanshu, D., Patel, D.		Authors: Ren, A., Rajashankar, K.R., Simanshu, D., Patel, D.

	Description: Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+		Description: Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+

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

OCA — Wed, 08 Oct 2014 06:34:07 GMT

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

←Older revision

Revision as of 06:34, 8 October 2014

OCA: New page: '''Unreleased structure''' The entry 4rgf is ON HOLD Authors: Ren, A., Rajashankar, K.R., Simanshu, D., Patel, D. Description: Crystal structure of the in-line aligned env22 twister ri...

OCA — Wed, 08 Oct 2014 06:34:05 GMT

New page: '''Unreleased structure''' The entry 4rgf is ON HOLD Authors: Ren, A., Rajashankar, K.R., Simanshu, D., Patel, D. Description: Crystal structure of the in-line aligned env22 twister ri...

New page

'''Unreleased structure'''

The entry 4rgf is ON HOLD

Authors: Ren, A., Rajashankar, K.R., Simanshu, D., Patel, D.

Description: Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+