6jq6 - Revision history

OCA at 10:39, 27 March 2024

OCA — Wed, 27 Mar 2024 10:39:13 GMT

←Older revision		Revision as of 10:39, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6jq6' size='340' side='right'caption='[[6jq6]], [[Resolution\|resolution]] 2.63Å' scene=''>		<StructureSection load='6jq6' size='340' side='right'caption='[[6jq6]], [[Resolution\|resolution]] 2.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jq6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQ6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JQ6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jq6]] is a 1 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=6JQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JQ6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</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]] 2.626Å</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=6jq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jq6 OCA], [~~http~~://pdbe.org/6jq6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jq6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jq6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jq6 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</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=6jq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jq6 OCA], [https://pdbe.org/6jq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jq6 RCSB], [https://www.ebi.ac.uk/pdbsum/6jq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jq6 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-A crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate. Strikingly, the catalytic pocket contains a cavity capable of accommodating both the modeled scissile phosphate and its flanking 5' nucleoside. The resulting modeled precatalytic conformation incorporates a splayed-apart alignment at the scissile phosphate, thereby providing structure-based insights into the in-line cleavage mechanism. We identify a guanine lining the catalytic pocket positioned to contribute to cleavage chemistry. The functional relevance of structure-based insights into hatchet ribozyme catalysis is strongly supported by cleavage assays monitoring the impact of selected nucleobase and atom-specific mutations on ribozyme activity.

-	Hatchet ribozyme structure and implications for cleavage mechanism.,Zheng L, Falschlunger C, Huang K, Mairhofer E, Yuan S, Wang J, Patel DJ, Micura R, Ren A Proc Natl Acad Sci U S A. 2019 May 28;116(22):10783-10791. doi:, 10.1073/pnas.1902413116. Epub 2019 May 14. PMID:31088965<ref>PMID:31088965</ref>	+	==See Also==
-		+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6jq6" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ren, A~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Zheng, L~~]]	+	[[Category: Ren A]]
-	[[Category: ~~Catalysis]]~~	+	[[Category: Zheng L]]
-	~~[[Category: Cleavage]]~~	+
-	~~[[Category: Hatchet]]~~	+
-	~~[[Category: Non-coding rna]]~~	+
-	~~[[Category: Ribozyme]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 05:37, 12 June 2019

OCA — Wed, 12 Jun 2019 05:37:15 GMT

←Older revision		Revision as of 05:37, 12 June 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6jq6 is ~~ON HOLD until Paper~~ Publication	+	==Hatchet Ribozyme Structure soaking with Ir(NH3)6+==
		+	<StructureSection load='6jq6' size='340' side='right'caption='[[6jq6]], [[Resolution\|resolution]] 2.63Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jq6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JQ6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</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=6jq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jq6 OCA], [http://pdbe.org/6jq6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jq6 RCSB], [http://www.ebi.ac.uk/pdbsum/6jq6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jq6 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-A crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate. Strikingly, the catalytic pocket contains a cavity capable of accommodating both the modeled scissile phosphate and its flanking 5' nucleoside. The resulting modeled precatalytic conformation incorporates a splayed-apart alignment at the scissile phosphate, thereby providing structure-based insights into the in-line cleavage mechanism. We identify a guanine lining the catalytic pocket positioned to contribute to cleavage chemistry. The functional relevance of structure-based insights into hatchet ribozyme catalysis is strongly supported by cleavage assays monitoring the impact of selected nucleobase and atom-specific mutations on ribozyme activity.

-	~~Authors~~:	+	Hatchet ribozyme structure and implications for cleavage mechanism.,Zheng L, Falschlunger C, Huang K, Mairhofer E, Yuan S, Wang J, Patel DJ, Micura R, Ren A Proc Natl Acad Sci U S A. 2019 May 28;116(22):10783-10791. doi:, 10.1073/pnas.1902413116. Epub 2019 May 14. PMID:31088965<ref>PMID:31088965</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6jq6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ren, A]]
		+	[[Category: Zheng, L]]
		+	[[Category: Catalysis]]
		+	[[Category: Cleavage]]
		+	[[Category: Hatchet]]
		+	[[Category: Non-coding rna]]
		+	[[Category: Ribozyme]]
		+	[[Category: Rna]]

OCA at 03:57, 17 April 2019

OCA — Wed, 17 Apr 2019 03:57:19 GMT

←Older revision		Revision as of 03:57, 17 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jq6 is ON HOLD	+	The entry 6jq6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6jq6" [edit=sysop:move=sysop]

OCA — Wed, 03 Apr 2019 04:30:20 GMT

Protected "6jq6" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:30, 3 April 2019

OCA: New page: '''Unreleased structure''' The entry 6jq6 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 03 Apr 2019 04:30:18 GMT

New page: '''Unreleased structure''' The entry 6jq6 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6jq6 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]