6xhw - Revision history

OCA at 10:52, 15 November 2023

OCA — Wed, 15 Nov 2023 10:52:38 GMT

←Older revision		Revision as of 10:52, 15 November 2023
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	==See Also==		==See Also==
-	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==

OCA at 14:52, 18 October 2023

OCA — Wed, 18 Oct 2023 14:52:48 GMT

←Older revision		Revision as of 14:52, 18 October 2023
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-	====	+	==Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution==
-	<StructureSection load='6xhw' size='340' side='right'caption='[[6xhw]]' scene=''>	+	<StructureSection load='6xhw' size='340' side='right'caption='[[6xhw]], [[Resolution\|resolution]] 2.50Å' 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'>[[6xhw]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XHW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XHW 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=6xhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xhw OCA], [https://pdbe.org/6xhw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xhw RCSB], [https://www.ebi.ac.uk/pdbsum/6xhw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xhw 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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=31H:3-DEOXY-3-[(N-FORMYL-L-METHIONYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31H</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=F3N:3-DEOXY-3-(L-PHENYLALANYLAMINO)ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>F3N</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=6xhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xhw OCA], [https://pdbe.org/6xhw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xhw RCSB], [https://www.ebi.ac.uk/pdbsum/6xhw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xhw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RL19_THET8 RL19_THET8] Contacts the 16S rRNA of the 30S subunit (part of bridge B6), connecting the 2 subunits.[HAMAP-Rule:MF_00402]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases. Here, we present the crystal structure of the Erm-dimethylated 70S ribosome at 2.4 A resolution, together with the structures of unmethylated 70S ribosome functional complexes alone or in combination with macrolides. Altogether, our structural data do not support previous models and, instead, suggest a principally new explanation of how A2058 dimethylation confers resistance to macrolides. Moreover, high-resolution structures of two macrolide antibiotics bound to the unmodified ribosome reveal a previously unknown role of the desosamine moiety in drug binding, laying a foundation for the rational knowledge-based design of macrolides that can overcome Erm-mediated resistance.
		+
		+	Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.,Svetlov MS, Syroegin EA, Aleksandrova EV, Atkinson GC, Gregory ST, Mankin AS, Polikanov YS Nat Chem Biol. 2021 Apr;17(4):412-420. doi: 10.1038/s41589-020-00715-0. Epub 2021 , Jan 18. PMID:33462493<ref>PMID:33462493</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xhw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Thermus thermophilus HB8]]
		+	[[Category: Aleksandrova EV]]
		+	[[Category: Atkinson GC]]
		+	[[Category: Gregory ST]]
		+	[[Category: Mankin AS]]
		+	[[Category: Polikanov YS]]
		+	[[Category: Svetlov MS]]
		+	[[Category: Syroegin EA]]

OCA at 11:08, 10 February 2021

OCA — Wed, 10 Feb 2021 11:08:20 GMT

←Older revision		Revision as of 11:08, 10 February 2021
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	<StructureSection load='6xhw' size='340' side='right'caption='[[6xhw]]' scene=''>		<StructureSection load='6xhw' size='340' side='right'caption='[[6xhw]]' 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 [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<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>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6xhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xhw OCA], [~~http~~://pdbe.org/6xhw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6xhw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6xhw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6xhw 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=6xhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xhw OCA], [https://pdbe.org/6xhw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xhw RCSB], [https://www.ebi.ac.uk/pdbsum/6xhw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xhw ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 10:31, 24 December 2020

OCA — Thu, 24 Dec 2020 10:31:39 GMT

←Older revision		Revision as of 10:31, 24 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6xhw ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6xhw' size='340' side='right'caption='[[6xhw]]' scene=''>
-	~~Authors~~: ~~Svetlov, M~~.S.~~, Syroegin, E~~.A.~~, Aleksandrova, E~~.V.~~, Atkinson, G~~.C.~~, Gregory, S.T~~., ~~Mankin, A~~.S.~~, Polikanov, Y~~.S.	+	== 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 [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Crystal structure of the A2058~~-~~unmethylated Thermus thermophilus 70S ribosome in complex with mRNA~~, ~~aminoacylated A-and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6xhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xhw OCA], [http://pdbe.org/6xhw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xhw RCSB], [http://www.ebi.ac.uk/pdbsum/6xhw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xhw ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Polikanov, Y~~.S]]	+	__TOC__
-	~~[[Category: Syroegin~~, ~~E.A]]~~	+	</StructureSection>
-	[~~[Category~~: ~~Gregory, S~~.T]]	+	[[Category: Large Structures]]
-	~~[[Category: Aleksandrova~~, ~~E.V]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Mankin, A~~.S]]	+
-	[[Category: ~~Svetlov, M.S~~]]	+
-	[[Category: ~~Atkinson, G.C~~]]	+

OCA at 05:26, 2 December 2020

OCA — Wed, 02 Dec 2020 05:26:51 GMT

←Older revision		Revision as of 05:26, 2 December 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xhw is ON HOLD	+	The entry 6xhw is ON HOLD until Paper Publication

	Authors: Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.		Authors: Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

OCA: Protected "6xhw" [edit=sysop:move=sysop]

OCA — Wed, 08 Jul 2020 10:47:39 GMT

Protected "6xhw" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:47, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6xhw is ON HOLD Authors: Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S. Descriptio...

OCA — Wed, 08 Jul 2020 10:47:38 GMT

New page: '''Unreleased structure''' The entry 6xhw is ON HOLD Authors: Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S. Descriptio...

New page

'''Unreleased structure'''

The entry 6xhw is ON HOLD

Authors: Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

Description: Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution
[[Category: Unreleased Structures]]
[[Category: Polikanov, Y.S]]
[[Category: Syroegin, E.A]]
[[Category: Gregory, S.T]]
[[Category: Aleksandrova, E.V]]
[[Category: Mankin, A.S]]
[[Category: Svetlov, M.S]]
[[Category: Atkinson, G.C]]