4e8m - Revision history

OCA at 14:55, 14 March 2024

2024-03-14T14:55:21Z

← Older revision		Revision as of 14:55, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e8m]] is a 1 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=4E8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8M FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e8m]] is a 1 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=4E8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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]] 3.5Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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=4e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8m OCA], [https://pdbe.org/4e8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8m RCSB], [https://www.ebi.ac.uk/pdbsum/4e8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8m 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=4e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8m OCA], [https://pdbe.org/4e8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8m RCSB], [https://www.ebi.ac.uk/pdbsum/4e8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8m ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Group II introns are self-splicing ribozymes that share a reaction mechanism and a common ancestor with the eukaryotic spliceosome, thereby providing a model system for understanding the chemistry of pre-mRNA splicing. Here we report 14 crystal structures of a group II intron at different stages of catalysis. We provide a detailed mechanism for the first step of splicing, we describe a reversible conformational change between the first and the second steps of splicing, and we present the ligand-free intron structure after splicing in an active state that corresponds to the retrotransposable form of the intron. During each reaction, the reactants are aligned and activated by a heteronuclear four-metal-ion center that contains a metal cluster and obligate monovalent cations, and they adopt a structural arrangement similar to that of protein endonucleases. Based on our data, we propose a model for the splicing cycle and show that it is applicable to the eukaryotic spliceosome.

	~~Visualizing Group II Intron Catalysis through the Stages of Splicing.,Marcia M, Pyle AM Cell. 2012 Oct 26;151(3):497-507. doi: 10.1016/j.cell.2012.09.033. PMID:23101623<ref>PMID:23101623</ref>~~

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e8m" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:57, 28 September 2022

2022-09-28T06:57:24Z

← Older revision		Revision as of 06:57, 28 September 2022
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	<StructureSection load='4e8m' size='340' side='right'caption='[[4e8m]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4e8m' size='340' side='right'caption='[[4e8m]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e8m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E8M FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e8m]] is a 1 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=4E8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e8k\|4e8k]], [[4e8n\|4e8n]], [[4e8p\|4e8p]], [[4e8q\|4e8q]], [[4e8r\|4e8r]], [[4e8t\|4e8t]], [[4e8v\|4e8v]]</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=4e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8m OCA], [https://pdbe.org/4e8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8m RCSB], [https://www.ebi.ac.uk/pdbsum/4e8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8m 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=4e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8m OCA], [~~http~~://pdbe.org/4e8m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e8m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e8m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8m 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: ~~Marcia, M~~]]		[[Category: Oceanobacillus iheyensis]]
	[[Category: ~~Pyle, A~~ M]]		[[Category: Marcia M]]
	[[Category: ~~Metalloenzyme]]~~		[[Category: Pyle AM]]
	~~[[Category: Retrotransposition]]~~
	~~[[Category: Ribozyme]]~~
	~~[[Category: Rna]]~~
	~~[[Category: Self-splicing~~]]

OCA at 07:32, 27 March 2019

2019-03-27T07:32:29Z

← Older revision		Revision as of 07:32, 27 March 2019
Line 1:		Line 1:

	==Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+==		==Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+==
	<StructureSection load='4e8m' size='340' side='right' caption='[[4e8m]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4e8m' size='340' side='right'caption='[[4e8m]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e8m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8M FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e8m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8M FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Marcia, M]]		[[Category: Marcia, M]]
	[[Category: Pyle, A M]]		[[Category: Pyle, A M]]

OCA at 02:45, 11 December 2016

2016-12-11T02:45:24Z

← Older revision		Revision as of 02:45, 11 December 2016
Line 1:		Line 1:

	==Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+==		==Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+==
	<StructureSection load='4e8m' size='340' side='right' caption='[[4e8m]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4e8m' size='340' side='right' caption='[[4e8m]], [[Resolution\|resolution]] 3.50Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e8k\|4e8k]], [[4e8n\|4e8n]], [[4e8p\|4e8p]], [[4e8q\|4e8q]], [[4e8r\|4e8r]], [[4e8t\|4e8t]], [[4e8v\|4e8v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e8k\|4e8k]], [[4e8n\|4e8n]], [[4e8p\|4e8p]], [[4e8q\|4e8q]], [[4e8r\|4e8r]], [[4e8t\|4e8t]], [[4e8v\|4e8v]]</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=4e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e8m RCSB], [http://www.ebi.ac.uk/pdbsum/4e8m 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=4e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8m OCA], [http://pdbe.org/4e8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e8m RCSB], [http://www.ebi.ac.uk/pdbsum/4e8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8m 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 4e8m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:41, 9 December 2014

2014-12-09T16:41:11Z

← Older revision		Revision as of 16:41, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~4e8m~~.~~jpg~~\|~~left~~\|~~200px~~]]		==Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+==
			<StructureSection load='4e8m' size='340' side='right' caption='[[4e8m]], [[Resolution\|resolution]] 3.50Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e8m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8M FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e8k\|4e8k]], [[4e8n\|4e8n]], [[4e8p\|4e8p]], [[4e8q\|4e8q]], [[4e8r\|4e8r]], [[4e8t\|4e8t]], [[4e8v\|4e8v]]</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=4e8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e8m RCSB], [http://www.ebi.ac.uk/pdbsum/4e8m PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Group II introns are self-splicing ribozymes that share a reaction mechanism and a common ancestor with the eukaryotic spliceosome, thereby providing a model system for understanding the chemistry of pre-mRNA splicing. Here we report 14 crystal structures of a group II intron at different stages of catalysis. We provide a detailed mechanism for the first step of splicing, we describe a reversible conformational change between the first and the second steps of splicing, and we present the ligand-free intron structure after splicing in an active state that corresponds to the retrotransposable form of the intron. During each reaction, the reactants are aligned and activated by a heteronuclear four-metal-ion center that contains a metal cluster and obligate monovalent cations, and they adopt a structural arrangement similar to that of protein endonucleases. Based on our data, we propose a model for the splicing cycle and show that it is applicable to the eukaryotic spliceosome.

	~~{{STRUCTURE_4e8m\| PDB=4e8m \| SCENE= }}~~		Visualizing Group II Intron Catalysis through the Stages of Splicing.,Marcia M, Pyle AM Cell. 2012 Oct 26;151(3):497-507. doi: 10.1016/j.cell.2012.09.033. PMID:23101623<ref>PMID:23101623</ref>

	~~===Structure~~ of ~~Oceanobacillus iheyensis group II intron in a ligand-free state in~~ the ~~presence~~ of ~~K+ and Mg2+===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
	==~~About this Structure~~==		<references/>
	~~[[4e8m]] is a 1 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=4E8M OCA].~~		__TOC__
	[[Category: Marcia, M.]]		</StructureSection>
	[[Category: Pyle, A M.]]		[[Category: Marcia, M]]
			[[Category: Pyle, A M]]
	[[Category: Metalloenzyme]]		[[Category: Metalloenzyme]]
	[[Category: Retrotransposition]]		[[Category: Retrotransposition]]

OCA at 06:49, 14 November 2012

2012-11-14T06:49:14Z

← Older revision		Revision as of 06:49, 14 November 2012
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		[[Image:4e8m.jpg\|left\|200px]]

	~~The entry~~ 4e8m ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4e8m\| PDB=4e8m \| SCENE= }}

	~~Authors: Marcia, M., Pyle, A.M.~~		===Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+===

	~~Description~~:
			==About this Structure==
			[[4e8m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8M OCA].
			[[Category: Marcia, M.]]
			[[Category: Pyle, A M.]]
			[[Category: Metalloenzyme]]
			[[Category: Retrotransposition]]
			[[Category: Ribozyme]]
			[[Category: Rna]]
			[[Category: Self-splicing]]

OCA at 05:46, 4 April 2012

2012-04-04T05:46:10Z

← Older revision		Revision as of 05:46, 4 April 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e8m is ON HOLD		The entry 4e8m is ON HOLD until Paper Publication

	Authors: Marcia, M., Pyle, A.M.		Authors: Marcia, M., Pyle, A.M.

	Description:		Description:

OCA: Protected "4e8m" [edit=sysop:move=sysop]

2012-03-28T07:24:39Z

Protected "4e8m" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:24, 28 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e8m is ON HOLD Authors: Marcia, M., Pyle, A.M. Description:

2012-03-28T07:24:38Z

New page: '''Unreleased structure''' The entry 4e8m is ON HOLD Authors: Marcia, M., Pyle, A.M. Description:

New page

'''Unreleased structure'''

The entry 4e8m is ON HOLD

Authors: Marcia, M., Pyle, A.M.

Description: