5j02 - Revision history

OCA at 10:40, 6 September 2023

OCA — Wed, 06 Sep 2023 10:40:29 GMT

←Older revision		Revision as of 10:40, 6 September 2023
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	<StructureSection load='5j02' size='340' side='right'caption='[[5j02]], [[Resolution\|resolution]] 3.49Å' scene=''>		<StructureSection load='5j02' size='340' side='right'caption='[[5j02]], [[Resolution\|resolution]] 3.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j02]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J02 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j02]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oceanobacillus_iheyensis Oceanobacillus iheyensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J02 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'>MG</scene~~>, ~~<scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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]] 3.493Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=6F7:3-DEOXY-5-METHYLURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>6F7</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6F7:3-DEOXY-5-METHYLURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>6F7</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=5j02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j02 OCA], [~~http~~://pdbe.org/5j02 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j02 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j02 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j02 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=5j02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j02 OCA], [https://pdbe.org/5j02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j02 RCSB], [https://www.ebi.ac.uk/pdbsum/5j02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j02 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Costa, M]]	+	[[Category: Oceanobacillus iheyensis]]
-	[[Category: Michel, F]]	+	[[Category: Costa M]]
-	[[Category: Monachello, D]]	+	[[Category: Michel F]]
-	[[Category: Walbott, H]]	+	[[Category: Monachello D]]
-	[[Category: Westhof, E]]	+	[[Category: Walbott H]]
-	~~[[Category: 2'-5' phosphodiester bond]]~~	+	[[Category: Westhof E]]
-	~~[[Category: Group ii intron]]~~	+
-	~~[[Category: Lariat]]~~	+
-	~~[[Category: Ribozyme]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna catalysis]]~~	+
-	~~[[Category: Self-splicing~~]]	+

OCA at 09:23, 30 October 2019

OCA — Wed, 30 Oct 2019 09:23:15 GMT

←Older revision		Revision as of 09:23, 30 October 2019
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	==Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.==		==Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.==
-	<StructureSection load='5j02' size='340' side='right' caption='[[5j02]], [[Resolution\|resolution]] 3.49Å' scene=''>	+	<StructureSection load='5j02' size='340' side='right'caption='[[5j02]], [[Resolution\|resolution]] 3.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5j02]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J02 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5j02]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J02 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5j02" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5j02" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Costa, M]]		[[Category: Costa, M]]
	[[Category: Michel, F]]		[[Category: Michel, F]]

OCA at 14:50, 22 December 2016

OCA — Thu, 22 Dec 2016 14:50:43 GMT

←Older revision		Revision as of 14:50, 22 December 2016
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	<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=5j02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j02 OCA], [http://pdbe.org/5j02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j02 RCSB], [http://www.ebi.ac.uk/pdbsum/5j02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j02 ProSAT]</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=5j02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j02 OCA], [http://pdbe.org/5j02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j02 RCSB], [http://www.ebi.ac.uk/pdbsum/5j02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j02 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 2'-5' branch of nuclear premessenger introns is believed to have been inherited from self-splicing group II introns, which are retrotransposons of bacterial origin. Our crystal structures at 3.4 and 3.5 angstrom of an excised group II intron in branched ("lariat") form show that the 2'-5' branch organizes a network of active-site tertiary interactions that position the intron terminal 3'-hydroxyl group into a configuration poised to initiate reverse splicing, the first step in retrotransposition. Moreover, the branchpoint and flanking helices must undergo a base-pairing switch after branch formation. A group II-based model of the active site of the nuclear splicing machinery (the spliceosome) is proposed. The crucial role of the lariat conformation in active-site assembly and catalysis explains its prevalence in modern splicing.
		+
		+	Crystal structures of a group II intron lariat primed for reverse splicing.,Costa M, Walbott H, Monachello D, Westhof E, Michel F Science. 2016 Dec 2;354(6316). pii: aaf9258. PMID:27934709<ref>PMID:27934709</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j02" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:18, 15 December 2016

OCA — Thu, 15 Dec 2016 19:18:01 GMT

←Older revision		Revision as of 19:18, 15 December 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5j02 is ~~ON HOLD until Paper Publication~~	+	==Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.==
-		+	<StructureSection load='5j02' size='340' side='right' caption='[[5j02]], [[Resolution\|resolution]] 3.49Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j02]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J02 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6F7:3-DEOXY-5-METHYLURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>6F7</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=5j02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j02 OCA], [http://pdbe.org/5j02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j02 RCSB], [http://www.ebi.ac.uk/pdbsum/5j02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j02 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Costa, M]]
		+	[[Category: Michel, F]]
		+	[[Category: Monachello, D]]
		+	[[Category: Walbott, H]]
		+	[[Category: Westhof, E]]
		+	[[Category: 2'-5' phosphodiester bond]]
		+	[[Category: Group ii intron]]
		+	[[Category: Lariat]]
		+	[[Category: Ribozyme]]
		+	[[Category: Rna]]
		+	[[Category: Rna catalysis]]
		+	[[Category: Self-splicing]]

OCA at 12:14, 10 August 2016

OCA — Wed, 10 Aug 2016 12:14:11 GMT

←Older revision		Revision as of 12:14, 10 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j02 is ON HOLD	+	The entry 5j02 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 14:55, 15 May 2016

OCA — Sun, 15 May 2016 14:55:28 GMT

←Older revision		Revision as of 14:55, 15 May 2016
Line 3:		Line 3:
	The entry 5j02 is ON HOLD		The entry 5j02 is ON HOLD

-	Authors: ~~Costa, M., Walbott, H., Monachello, D., Westhof, E., Michel, F.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Costa, M]]
-	[[Category: Michel, F]]
-	[[Category: Walbott, H]]
-	[[Category: Monachello, D]]
-	[[Category: Westhof, E]]

OCA: Protected "5j02" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:14:25 GMT

Protected "5j02" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:14, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j02 is ON HOLD Authors: Costa, M., Walbott, H., Monachello, D., Westhof, E., Michel, F. Description: Category: Unreleased Structures [[Catego...

OCA — Wed, 11 May 2016 01:14:24 GMT

New page: '''Unreleased structure''' The entry 5j02 is ON HOLD Authors: Costa, M., Walbott, H., Monachello, D., Westhof, E., Michel, F. Description: Category: Unreleased Structures [[Catego...

New page

'''Unreleased structure'''

The entry 5j02 is ON HOLD

Authors: Costa, M., Walbott, H., Monachello, D., Westhof, E., Michel, F.

Description:
[[Category: Unreleased Structures]]
[[Category: Costa, M]]
[[Category: Michel, F]]
[[Category: Walbott, H]]
[[Category: Monachello, D]]
[[Category: Westhof, E]]