1rmn - Revision history

OCA at 08:24, 14 February 2024

OCA — Wed, 14 Feb 2024 08:24:16 GMT

←Older revision		Revision as of 08:24, 14 February 2024
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [https://pdbe.org/1rmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [https://www.ebi.ac.uk/pdbsum/1rmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmn 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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [https://pdbe.org/1rmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [https://www.ebi.ac.uk/pdbsum/1rmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmn ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study the structure of the ribozyme in solution in order to establish the relative spatial orientation of the three constituent Watson-Crick base-paired helical segments. Synthetic constructs were labeled with the fluorescence donor (5-carboxyfluorescein) and acceptor (5-carboxytetramethylrhodamine) located at the ends of the strands constituting the ribozyme molecule. The acceptor helix in helix pairs I and III and in II and III was varied in length from 5 to 11 and 5 to 9 base pairs, respectively, and the FRET efficiencies were determined and correlated with a reference set of labeled RNA duplexes. The FRET efficiencies were predicted on the basis of vector algebra analysis, as a function of the relative helical orientations in the ribozyme constructs, and compared with experimental values. The data were consistent with a Y-shaped arrangement of the ribozyme with helices I and II in close proximity and helix III pointing away. These orientational constraints were used for molecular modeling of a three-dimensional structure of the complete ribozyme.
-
-	A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements.,Tuschl T, Gohlke C, Jovin TM, Westhof E, Eckstein F Science. 1994 Nov 4;266(5186):785-9. PMID:7973630<ref>PMID:7973630</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1rmn" 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 21:34, 28 June 2023

OCA — Wed, 28 Jun 2023 21:34:02 GMT

←Older revision		Revision as of 21:34, 28 June 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMN FirstGlance]. <br>
-	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [https://pdbe.org/1rmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [https://www.ebi.ac.uk/pdbsum/1rmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmn ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Fluorescence transfer</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [https://pdbe.org/1rmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [https://www.ebi.ac.uk/pdbsum/1rmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:

	==See Also==		==See Also==
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Eckstein, F]]	+	[[Category: Eckstein F]]
-	[[Category: Gohlke, C]]	+	[[Category: Gohlke C]]
-	[[Category: Jovin~~, T M~~]]	+	[[Category: Jovin TM]]
-	[[Category: Tuschl, T]]	+	[[Category: Tuschl T]]
-	[[Category: Westhof, E]]	+	[[Category: Westhof E]]

OCA at 07:18, 22 September 2021

OCA — Wed, 22 Sep 2021 07:18:29 GMT

←Older revision		Revision as of 07:18, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1rmn' size='340' side='right'caption='[[1rmn]]' scene=''>		<StructureSection load='1rmn' size='340' side='right'caption='[[1rmn]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMN FirstGlance]. <br>
-	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [~~http~~://pdbe.org/1rmn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rmn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmn ProSAT]</span></td></tr>	+	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [https://pdbe.org/1rmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [https://www.ebi.ac.uk/pdbsum/1rmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:30, 11 December 2019

OCA — Wed, 11 Dec 2019 19:30:33 GMT

←Older revision		Revision as of 19:30, 11 December 2019
Line 1:		Line 1:

	==A THREE-DIMENSIONAL MODEL FOR THE HAMMERHEAD RIBOZYME BASED ON FLUORESCENCE MEASUREMENTS==		==A THREE-DIMENSIONAL MODEL FOR THE HAMMERHEAD RIBOZYME BASED ON FLUORESCENCE MEASUREMENTS==
-	<StructureSection load='1rmn' size='340' side='right' caption='[[1rmn]]' scene=''>	+	<StructureSection load='1rmn' size='340' side='right'caption='[[1rmn]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Eckstein, F]]		[[Category: Eckstein, F]]
	[[Category: Gohlke, C]]		[[Category: Gohlke, C]]

OCA at 07:01, 8 March 2018

OCA — Thu, 08 Mar 2018 07:01:49 GMT

←Older revision		Revision as of 07:01, 8 March 2018
Line 1:		Line 1:
		+
	==A THREE-DIMENSIONAL MODEL FOR THE HAMMERHEAD RIBOZYME BASED ON FLUORESCENCE MEASUREMENTS==		==A THREE-DIMENSIONAL MODEL FOR THE HAMMERHEAD RIBOZYME BASED ON FLUORESCENCE MEASUREMENTS==
	<StructureSection load='1rmn' size='340' side='right' caption='[[1rmn]]' scene=''>		<StructureSection load='1rmn' size='340' side='right' caption='[[1rmn]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>
-	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [http://pdbe.org/1rmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [http://www.ebi.ac.uk/pdbsum/1rmn PDBsum]</span></td></tr>	+	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [http://pdbe.org/1rmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [http://www.ebi.ac.uk/pdbsum/1rmn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:40, 11 September 2015

OCA — Fri, 11 Sep 2015 02:40:26 GMT

←Older revision		Revision as of 02:40, 11 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>
-	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [http://www.ebi.ac.uk/pdbsum/1rmn PDBsum]</span></td></tr>	+	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [http://pdbe.org/1rmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [http://www.ebi.ac.uk/pdbsum/1rmn PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 13:
	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 1rmn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:11, 6 January 2015

OCA — Tue, 06 Jan 2015 08:11:52 GMT

←Older revision		Revision as of 08:11, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>
-	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [http://www.ebi.ac.uk/pdbsum/1rmn PDBsum]</span></td></tr>	+	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [http://www.ebi.ac.uk/pdbsum/1rmn PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Eckstein, F.]]	+	[[Category: Eckstein, F]]
-	[[Category: Gohlke, C.]]	+	[[Category: Gohlke, C]]
-	[[Category: Jovin, T M.]]	+	[[Category: Jovin, T M]]
-	[[Category: Tuschl, T.]]	+	[[Category: Tuschl, T]]
-	[[Category: Westhof, E.]]	+	[[Category: Westhof, E]]

OCA at 22:56, 28 September 2014

OCA — Sun, 28 Sep 2014 22:56:17 GMT

←Older revision		Revision as of 22:56, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1rmn.~~png\|left\|200px~~]]	+	==A THREE-DIMENSIONAL MODEL FOR THE HAMMERHEAD RIBOZYME BASED ON FLUORESCENCE MEASUREMENTS==
		+	<StructureSection load='1rmn' size='340' side='right' caption='[[1rmn]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMN FirstGlance]. <br>
		+	</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=1rmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmn RCSB], [http://www.ebi.ac.uk/pdbsum/1rmn PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study the structure of the ribozyme in solution in order to establish the relative spatial orientation of the three constituent Watson-Crick base-paired helical segments. Synthetic constructs were labeled with the fluorescence donor (5-carboxyfluorescein) and acceptor (5-carboxytetramethylrhodamine) located at the ends of the strands constituting the ribozyme molecule. The acceptor helix in helix pairs I and III and in II and III was varied in length from 5 to 11 and 5 to 9 base pairs, respectively, and the FRET efficiencies were determined and correlated with a reference set of labeled RNA duplexes. The FRET efficiencies were predicted on the basis of vector algebra analysis, as a function of the relative helical orientations in the ribozyme constructs, and compared with experimental values. The data were consistent with a Y-shaped arrangement of the ribozyme with helices I and II in close proximity and helix III pointing away. These orientational constraints were used for molecular modeling of a three-dimensional structure of the complete ribozyme.

-	~~{{STRUCTURE_1rmn\| PDB=1rmn \| SCENE= }}~~	+	A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements.,Tuschl T, Gohlke C, Jovin TM, Westhof E, Eckstein F Science. 1994 Nov 4;266(5186):785-9. PMID:7973630<ref>PMID:7973630</ref>

-	~~===A THREE-DIMENSIONAL MODEL FOR THE HAMMERHEAD RIBOZYME BASED ON FLUORESCENCE MEASUREMENTS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7973630}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1rmn]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1RMN OCA].~~	+

	==See Also==		==See Also==
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007973630<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Eckstein, F.]]		[[Category: Eckstein, F.]]
	[[Category: Gohlke, C.]]		[[Category: Gohlke, C.]]

OCA at 15:22, 20 October 2012

OCA — Sat, 20 Oct 2012 15:22:03 GMT

←Older revision		Revision as of 15:22, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1rmn]] is a 1 chain structure ~~of [[Ribozyme]]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA].	+	[[1rmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMN OCA].

	==See Also==		==See Also==

OCA: Protected "1rmn" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 18:09:41 GMT

Protected "1rmn" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:09, 26 July 2012