7eqj - Revision history

OCA at 16:59, 29 November 2023

OCA — Wed, 29 Nov 2023 16:59:51 GMT

←Older revision		Revision as of 16:59, 29 November 2023
Line 1:		Line 1:

	==crystal structure of E. coli Valine tRNA==		==crystal structure of E. coli Valine tRNA==
-	<StructureSection load='7eqj' size='340' side='right'caption='[[7eqj]]' scene=''>	+	<StructureSection load='7eqj' size='340' side='right'caption='[[7eqj]], [[Resolution\|resolution]] 2.04Å' 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=7EQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7eqj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EQJ 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=7eqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eqj OCA], [https://pdbe.org/7eqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eqj RCSB], [https://www.ebi.ac.uk/pdbsum/7eqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eqj 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]] 2.043Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7eqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eqj OCA], [https://pdbe.org/7eqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eqj RCSB], [https://www.ebi.ac.uk/pdbsum/7eqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eqj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During protein synthesis on ribosome, tRNA recognizes its cognate codon of mRNA through base-pairing with the anticodon. The 5'-end nucleotide of the anticodon is capable of wobble base-pairing, offering a molecular basis for codon degeneracy. The wobble nucleotide is often targeted for post-transcriptional modification, which affects the specificity and fidelity of the decoding process. Flipping-out of a wobble nucleotide in the anticodon loop has been proposed to be necessary for modifying enzymes to access the target nucleotide, which has been captured in selective structures of protein-bound complexes. Meanwhile, all other structures of free or ribosome-bound tRNA display anticodon bases arranged in stacked conformation. We report the X-ray crystal structure of unbound tRNA(Val1) to a 2.04 A resolution showing two different conformational states of wobble uridine in the anticodon loop, one stacked on the neighboring base and the other swiveled out toward solvent. In addition, the structure reveals a rare magnesium ion coordination to the nitrogen atom of a nucleobase, which has been sampled very rarely among known structures of nucleic acids.
		+
		+	Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNA(Val).,Jeong H, Kim J RNA. 2021 Nov;27(11):1330-1338. doi: 10.1261/rna.078863.121. Epub 2021 Jul 27. PMID:34315814<ref>PMID:34315814</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7eqj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Jeong H]]		[[Category: Jeong H]]
	[[Category: Kim J]]		[[Category: Kim J]]

OCA at 07:27, 19 January 2022

OCA — Wed, 19 Jan 2022 07:27:23 GMT

←Older revision		Revision as of 07:27, 19 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

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

OCA at 08:41, 19 May 2021

OCA — Wed, 19 May 2021 08:41:50 GMT

←Older revision		Revision as of 08:41, 19 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kim, J., Jeong, H.		Authors: Kim, J., Jeong, H.

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

OCA — Wed, 12 May 2021 08:04:15 GMT

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

←Older revision

Revision as of 08:04, 12 May 2021

OCA: New page: '''Unreleased structure''' The entry 7eqj is ON HOLD Authors: Kim, J., Jeong, H. Description: crystal structure of E. coli Valine tRNA Category: Unreleased Structures [[Category: K...

OCA — Wed, 12 May 2021 08:04:14 GMT

New page: '''Unreleased structure''' The entry 7eqj is ON HOLD Authors: Kim, J., Jeong, H. Description: crystal structure of E. coli Valine tRNA Category: Unreleased Structures [[Category: K...

New page

'''Unreleased structure'''

The entry 7eqj is ON HOLD

Authors: Kim, J., Jeong, H.

Description: crystal structure of E. coli Valine tRNA
[[Category: Unreleased Structures]]
[[Category: Kim, J]]
[[Category: Jeong, H]]