7urm - Revision history

OCA at 06:26, 26 October 2022

OCA — Wed, 26 Oct 2022 06:26:46 GMT

←Older revision		Revision as of 06:26, 26 October 2022
Line 1:		Line 1:

	==allo-tRNAUTu1A in the P site of the E. coli ribosome==		==allo-tRNAUTu1A in the P site of the E. coli ribosome==
-	<StructureSection load='7urm' size='340' side='right'caption='[[7urm]]' scene=''>	+	<StructureSection load='7urm' size='340' side='right'caption='[[7urm]], [[Resolution\|resolution]] 3.00Å' 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=7URM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7URM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7urm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Metagenome Metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7URM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7URM 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=7urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7urm OCA], [https://pdbe.org/7urm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7urm RCSB], [https://www.ebi.ac.uk/pdbsum/7urm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7urm 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=7urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7urm OCA], [https://pdbe.org/7urm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7urm RCSB], [https://www.ebi.ac.uk/pdbsum/7urm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7urm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNAUTu1, a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNAUTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.
		+
		+	Uncovering translation roadblocks during the development of a synthetic tRNA.,Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnkovic A, Ehrenberg M, Puglisi EV, Soll D, Puglisi J Nucleic Acids Res. 2022 Jul 27. pii: 6649945. doi: 10.1093/nar/gkac576. PMID:35882385<ref>PMID:35882385</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7urm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Metagenome]]
	[[Category: Acosta-Reyes FJ]]		[[Category: Acosta-Reyes FJ]]
	[[Category: Choi J]]		[[Category: Choi J]]

OCA at 05:00, 10 August 2022

OCA — Wed, 10 Aug 2022 05:00:51 GMT

←Older revision		Revision as of 05:00, 10 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7urm ~~is ON HOLD until Paper Publication~~	+	==allo-tRNAUTu1A in the P site of the E. coli ribosome==
-		+	<StructureSection load='7urm' size='340' side='right'caption='[[7urm]]' scene=''>
-	~~Authors~~: ~~Zhang, J~~.~~, Prabhakar, A~~.~~, Krahn, N~~.~~, Vargas~~-~~Rodriguez, O~~.~~, Krupkin, M~~.~~, Fu, Z~~.~~, Acosta-Reyes, F~~.J.~~, Ge, X~~., ~~Choi, J~~.~~, Crnkovic, A~~., ~~Ehrenberg, M~~., ~~Viani Puglisi, E~~., ~~Soll, D~~., ~~Puglisi, J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7URM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7URM FirstGlance]. <br>
-	~~Description: allo~~-~~tRNAUTu1A in the P site of the E~~. ~~coli ribosome~~	+	</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=7urm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7urm OCA], [https://pdbe.org/7urm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7urm RCSB], [https://www.ebi.ac.uk/pdbsum/7urm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7urm ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Ehrenberg, M~~]]	+	__TOC__
-	[[Category: Choi, J]]	+	</StructureSection>
-	[[Category: ~~Krahn, N~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Prabhakar, A~~]]	+	[[Category: Acosta-Reyes FJ]]
-	[[Category: Fu, Z]]	+	[[Category: Choi J]]
-	[[Category: ~~Viani Puglisi, E~~]]	+	[[Category: Crnkovic A]]
-	[[Category: ~~Ge, X~~]]	+	[[Category: Ehrenberg M]]
-	[[Category: Krupkin, M]]	+	[[Category: Fu Z]]
-	[[Category: ~~Acosta-Reyes, F.~~J]]	+	[[Category: Ge X]]
-	[[Category: ~~Crnkovic, A~~]]	+	[[Category: Krahn N]]
-	[[Category: Vargas-Rodriguez, O]]	+	[[Category: Krupkin M]]
-	[[Category: Puglisi~~, J~~]]	+	[[Category: Prabhakar A]]
-	[[Category: Zhang, J]]	+	[[Category: Puglisi J]]
-	~~[[Category: Soll, D~~]]	+	[[Category: Soll D]]
		+	[[Category: Vargas-Rodriguez O]]
		+	[[Category: Viani Puglisi E]]
		+	[[Category: Zhang J]]

OCA at 04:46, 12 May 2022

OCA — Thu, 12 May 2022 04:46:37 GMT

←Older revision		Revision as of 04:46, 12 May 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zhang, J., Prabhakar, A., Krahn, N., Vargas-Rodriguez, O., Krupkin, M., Fu, Z., Acosta-Reyes, F.J., Ge, X., Choi, J., Crnkovic, A., Ehrenberg, M., Viani Puglisi, E., Soll, D., Puglisi, J.		Authors: Zhang, J., Prabhakar, A., Krahn, N., Vargas-Rodriguez, O., Krupkin, M., Fu, Z., Acosta-Reyes, F.J., Ge, X., Choi, J., Crnkovic, A., Ehrenberg, M., Viani Puglisi, E., Soll, D., Puglisi, J.
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	[[Category: Krahn, N]]		[[Category: Krahn, N]]
	[[Category: Prabhakar, A]]		[[Category: Prabhakar, A]]
-	[[Category: Viani Puglisi, E]]
-	[[Category: Acosta-Reyes, F.J]]
-	[[Category: Crnkovic, A]]
	[[Category: Fu, Z]]		[[Category: Fu, Z]]
		+	[[Category: Viani Puglisi, E]]
	[[Category: Ge, X]]		[[Category: Ge, X]]
	[[Category: Krupkin, M]]		[[Category: Krupkin, M]]
		+	[[Category: Acosta-Reyes, F.J]]
		+	[[Category: Crnkovic, A]]
	[[Category: Vargas-Rodriguez, O]]		[[Category: Vargas-Rodriguez, O]]
	[[Category: Puglisi, J]]		[[Category: Puglisi, J]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]
	[[Category: Soll, D]]		[[Category: Soll, D]]

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

OCA — Wed, 04 May 2022 11:31:26 GMT

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

←Older revision

Revision as of 11:31, 4 May 2022

OCA: New page: '''Unreleased structure''' The entry 7urm is ON HOLD Authors: Zhang, J., Prabhakar, A., Krahn, N., Vargas-Rodriguez, O., Krupkin, M., Fu, Z., Acosta-Reyes, F.J., Ge, X., Choi, J., Crnko...

OCA — Wed, 04 May 2022 11:31:25 GMT

New page: '''Unreleased structure''' The entry 7urm is ON HOLD Authors: Zhang, J., Prabhakar, A., Krahn, N., Vargas-Rodriguez, O., Krupkin, M., Fu, Z., Acosta-Reyes, F.J., Ge, X., Choi, J., Crnko...

New page

'''Unreleased structure'''

The entry 7urm is ON HOLD

Authors: Zhang, J., Prabhakar, A., Krahn, N., Vargas-Rodriguez, O., Krupkin, M., Fu, Z., Acosta-Reyes, F.J., Ge, X., Choi, J., Crnkovic, A., Ehrenberg, M., Viani Puglisi, E., Soll, D., Puglisi, J.

Description: allo-tRNAUTu1A in the P site of the E. coli ribosome
[[Category: Unreleased Structures]]
[[Category: Ehrenberg, M]]
[[Category: Choi, J]]
[[Category: Krahn, N]]
[[Category: Prabhakar, A]]
[[Category: Viani Puglisi, E]]
[[Category: Acosta-Reyes, F.J]]
[[Category: Crnkovic, A]]
[[Category: Fu, Z]]
[[Category: Ge, X]]
[[Category: Krupkin, M]]
[[Category: Vargas-Rodriguez, O]]
[[Category: Puglisi, J]]
[[Category: Zhang, J]]
[[Category: Soll, D]]