OCA at 15:20, 18 October 2023

OCA — Wed, 18 Oct 2023 15:20:12 GMT

←Older revision		Revision as of 15:20, 18 October 2023
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-	====	+	==GsI-IIC RT Template-Switching Complex (twinned)==
-	<StructureSection load='7k9y' size='340' side='right'caption='[[7k9y]]' scene=''>	+	<StructureSection load='7k9y' size='340' side='right'caption='[[7k9y]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k9y]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K9Y 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=7k9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9y OCA], [https://pdbe.org/7k9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k9y RCSB], [https://www.ebi.ac.uk/pdbsum/7k9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9y ProSAT]</span></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]] 3.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7k9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9y OCA], [https://pdbe.org/7k9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k9y RCSB], [https://www.ebi.ac.uk/pdbsum/7k9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9y ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E2GM63_GEOSE E2GM63_GEOSE]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Reverse transcriptases (RTs) can switch template strands during complementary DNA synthesis, enabling them to join discontinuous nucleic acid sequences. Template switching (TS) plays crucial roles in retroviral replication and recombination, is used for adapter addition in RNA-Seq, and may contribute to retroelement fitness by increasing evolutionary diversity and enabling continuous complementary DNA synthesis on damaged templates. Here, we determined an X-ray crystal structure of a TS complex of a group II intron RT bound simultaneously to an acceptor RNA and donor RNA template-DNA primer heteroduplex with a 1-nt 3'-DNA overhang. The structure showed that the 3' end of the acceptor RNA binds in a pocket formed by an N-terminal extension present in non-long terminal repeat-retroelement RTs and the RT fingertips loop, with the 3' nucleotide of the acceptor base paired to the 1-nt 3'-DNA overhang and its penultimate nucleotide base paired to the incoming dNTP at the RT active site. Analysis of structure-guided mutations identified amino acids that contribute to acceptor RNA binding and a phenylalanine residue near the RT active site that mediates nontemplated nucleotide addition. Mutation of the latter residue decreased multiple sequential template switches in RNA-Seq. Our results provide new insights into the mechanisms of TS and nontemplated nucleotide addition by RTs, suggest how these reactions could be improved for RNA-Seq, and reveal common structural features for TS by non-long terminal repeat-retroelement RTs and viral RNA-dependent RNA polymerases.
		+
		+	Structural basis for template switching by a group II intron-encoded non-LTR-retroelement reverse transcriptase.,Lentzsch AM, Stamos JL, Yao J, Russell R, Lambowitz AM J Biol Chem. 2021 Aug;297(2):100971. doi: 10.1016/j.jbc.2021.100971. Epub 2021 , Jul 17. PMID:34280434<ref>PMID:34280434</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7k9y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Lentzsch AM]]
		+	[[Category: Stamos JL]]

OCA at 06:08, 18 August 2021

OCA — Wed, 18 Aug 2021 06:08:05 GMT

←Older revision		Revision as of 06:08, 18 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7k9y ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7k9y' size='340' side='right'caption='[[7k9y]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7k9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k9y OCA], [https://pdbe.org/7k9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k9y RCSB], [https://www.ebi.ac.uk/pdbsum/7k9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k9y ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:34, 4 November 2020

OCA — Wed, 04 Nov 2020 05:34:38 GMT

←Older revision		Revision as of 05:34, 4 November 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7k9y is ON HOLD	+	The entry 7k9y is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7k9y" [edit=sysop:move=sysop]

OCA — Wed, 07 Oct 2020 04:50:04 GMT

Protected "7k9y" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:50, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7k9y is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Oct 2020 04:50:02 GMT

New page: '''Unreleased structure''' The entry 7k9y is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7k9y is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7k9y - Revision history

OCA at 15:20, 18 October 2023

OCA at 06:08, 18 August 2021

OCA at 05:34, 4 November 2020

OCA: Protected "7k9y" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7k9y is ON HOLD Authors: Description: Category: Unreleased Structures