OCA at 11:11, 15 November 2023

OCA — Wed, 15 Nov 2023 11:11:06 GMT

←Older revision		Revision as of 11:11, 15 November 2023
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-	====	+	==wild-type Escherichia coli stalled ribosome with antibiotic linezolid==
-	<StructureSection load='7s1g' size='340' side='right'caption='[[7s1g]]' scene=''>	+	<StructureSection load='7s1g' size='340' side='right'caption='[[7s1g]], [[Resolution\|resolution]] 2.48Å' 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'>[[7s1g]] is a 10 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=7S1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S1G 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=7s1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s1g OCA], [https://pdbe.org/7s1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s1g RCSB], [https://www.ebi.ac.uk/pdbsum/7s1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s1g ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 2.48Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=4D4:(2S,3R)-2-AZANYL-5-CARBAMIMIDAMIDO-3-OXIDANYL-PENTANOIC+ACID'>4D4</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=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</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=ZLD:N-{[(5S)-3-(3-FLUORO-4-MORPHOLIN-4-YLPHENYL)-2-OXO-1,3-OXAZOLIDIN-5-YL]METHYL}ACETAMIDE'>ZLD</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=7s1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s1g OCA], [https://pdbe.org/7s1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s1g RCSB], [https://www.ebi.ac.uk/pdbsum/7s1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s1g ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. However, the molecular basis for context-specificity has not been elucidated. Here we show that the second-generation oxazolidinone radezolid also induces stalling with a penultimate alanine, and we determine high-resolution cryo-EM structures of linezolid- and radezolid-stalled ribosome complexes to explain their mechanism of action. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling due to repositioning of the modified nucleotide. Together, our findings provide molecular understanding for the context-specificity of oxazolidinones.
		+
		+	Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.,Tsai K, Stojkovic V, Lee DJ, Young ID, Szal T, Klepacki D, Vazquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG Nat Struct Mol Biol. 2022 Feb;29(2):162-171. doi: 10.1038/s41594-022-00723-9. , Epub 2022 Feb 14. PMID:35165456<ref>PMID:35165456</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7s1g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Fraser JS]]
		+	[[Category: Galonic Fujimori D]]
		+	[[Category: Lee DJ]]
		+	[[Category: Stojkovic V]]
		+	[[Category: Tsai K]]
		+	[[Category: Young ID]]

OCA at 13:39, 17 November 2021

OCA — Wed, 17 Nov 2021 13:39:41 GMT

←Older revision		Revision as of 13:39, 17 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7s1g ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7s1g' size='340' side='right'caption='[[7s1g]]' scene=''>
-	~~Authors~~: ~~Young, I~~.D.~~, Stojkovic, V~~.~~, Tsai, K~~.~~, Lee, D~~.J.~~, Fraser, J.S., Galonic Fujimori, D~~.	+	== 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~~: ~~wild-type Escherichia coli stalled ribosome with antibiotic linezolid~~	+	</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=7s1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s1g OCA], [https://pdbe.org/7s1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s1g RCSB], [https://www.ebi.ac.uk/pdbsum/7s1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s1g ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Stojkovic, V]~~]	+	__TOC__
-	[~~[Category~~: ~~Fraser, J~~.S]]	+	</StructureSection>
-	[~~[Category~~: ~~Young, I~~.D]]	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Lee~~, D.J]]	+	[[Category: Z-disk]]
-	[[Category: ~~Galonic Fujimori, D~~]]	+
-	[[Category: ~~Tsai, K~~]]	+

OCA: Protected "7s1g" [edit=sysop:move=sysop]

OCA — Wed, 08 Sep 2021 07:53:23 GMT

Protected "7s1g" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:53, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7s1g is ON HOLD Authors: Young, I.D., Stojkovic, V., Tsai, K., Lee, D.J., Fraser, J.S., Galonic Fujimori, D. Description: wild-type Escherichia col...

OCA — Wed, 08 Sep 2021 07:53:22 GMT

New page: '''Unreleased structure''' The entry 7s1g is ON HOLD Authors: Young, I.D., Stojkovic, V., Tsai, K., Lee, D.J., Fraser, J.S., Galonic Fujimori, D. Description: wild-type Escherichia col...

New page

'''Unreleased structure'''

The entry 7s1g is ON HOLD

Authors: Young, I.D., Stojkovic, V., Tsai, K., Lee, D.J., Fraser, J.S., Galonic Fujimori, D.

Description: wild-type Escherichia coli stalled ribosome with antibiotic linezolid
[[Category: Unreleased Structures]]
[[Category: Stojkovic, V]]
[[Category: Fraser, J.S]]
[[Category: Young, I.D]]
[[Category: Lee, D.J]]
[[Category: Galonic Fujimori, D]]
[[Category: Tsai, K]]

7s1g - Revision history

OCA at 11:11, 15 November 2023

OCA at 13:39, 17 November 2021

OCA: Protected "7s1g" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7s1g is ON HOLD Authors: Young, I.D., Stojkovic, V., Tsai, K., Lee, D.J., Fraser, J.S., Galonic Fujimori, D. Description: wild-type Escherichia col...