OCA at 08:01, 6 December 2023

OCA — Wed, 06 Dec 2023 08:01:53 GMT

←Older revision		Revision as of 08:01, 6 December 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8jdl is ~~ON HOLD until Paper~~ Publication	+	==Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)==
		+	<StructureSection load='8jdl' size='340' side='right'caption='[[8jdl]], [[Resolution\|resolution]] 2.42Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8jdl]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8JDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JDL FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 2.42Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3AU:3-[(3S)-3-AMINO-3-CARBOXYPROPYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>3AU</scene>, <scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=56B:2-AMINO-5-({[(1S,4S,5R)-4,5-DIHYDROXYCYCLOPENT-2-EN-1-YL]AMINO}METHYL)-7-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE'>56B</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=B8N:(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic+acid'>B8N</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=UY1:2-O-methylpseudouridine-5-monophosphate'>UY1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8jdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8jdl OCA], [https://pdbe.org/8jdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8jdl RCSB], [https://www.ebi.ac.uk/pdbsum/8jdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8jdl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RL8_HUMAN RL8_HUMAN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.

-	~~Authors~~:	+	Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.,Zhao X, Ma D, Ishiguro K, Saito H, Akichika S, Matsuzawa I, Mito M, Irie T, Ishibashi K, Wakabayashi K, Sakaguchi Y, Yokoyama T, Mishima Y, Shirouzu M, Iwasaki S, Suzuki T, Suzuki T Cell. 2023 Nov 17:S0092-8674(23)01177-7. doi: 10.1016/j.cell.2023.10.026. PMID:37992713<ref>PMID:37992713</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8jdl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Ishiguro K]]
		+	[[Category: Shirouzu M]]
		+	[[Category: Suzuki T]]
		+	[[Category: Yokoyama T]]

OCA at 03:52, 12 July 2023

OCA — Wed, 12 Jul 2023 03:52:01 GMT

←Older revision		Revision as of 03:52, 12 July 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8jdl is ON HOLD	+	The entry 8jdl is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8jdl" [edit=sysop:move=sysop]

OCA — Thu, 25 May 2023 02:26:05 GMT

Protected "8jdl" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:26, 25 May 2023

OCA: New page: '''Unreleased structure''' The entry 8jdl is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 25 May 2023 02:26:04 GMT

New page: '''Unreleased structure''' The entry 8jdl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8jdl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

8jdl - Revision history

OCA at 08:01, 6 December 2023

OCA at 03:52, 12 July 2023

OCA: Protected "8jdl" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8jdl is ON HOLD Authors: Description: Category: Unreleased Structures