8fc2 - Revision history

OCA at 06:35, 12 February 2025

2025-02-12T06:35:09Z

← Older revision		Revision as of 06:35, 12 February 2025
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	<table><tr><td colspan='2'>[[8fc2]] 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=8FC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8FC2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8fc2]] 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=8FC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8FC2 FirstGlance]. <br>
	</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>		</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=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=HGR:HYGROMYCIN+A'>HGR</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=ZIT:AZITHROMYCIN'>ZIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=HGR:HYGROMYCIN+A'>HGR</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=ZIT:AZITHROMYCIN'>ZIT</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=8fc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8fc2 OCA], [https://pdbe.org/8fc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8fc2 RCSB], [https://www.ebi.ac.uk/pdbsum/8fc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8fc2 ProSAT]</span></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=8fc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8fc2 OCA], [https://pdbe.org/8fc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8fc2 RCSB], [https://www.ebi.ac.uk/pdbsum/8fc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8fc2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/~~RL3_THET8 RL3_THET8~~] ~~One~~ of the ~~primary rRNA binding proteins~~, ~~it binds directly near~~ the 3'-~~end~~ of the ~~23S rRNA~~, ~~where it nucleates assembly~~ of the ~~50S subunit~~ (~~By similarity~~).~~[HAMAP~~-~~Rule~~:~~MF_01325_B]~~		[https://www.uniprot.org/uniprot/RL33_THET8 RL33_THET8] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00294] Contacts the E site tRNA.[HAMAP-Rule:MF_00294]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The ever-growing rise of antibiotic resistance among bacterial pathogens is one of the top healthcare threats today. Although combination antibiotic therapies represent a potential approach to more efficiently combat infections caused by susceptible and drug-resistant bacteria, only a few known drug pairs exhibit synergy/cooperativity in killing bacteria. Here, we discover that well-known ribosomal antibiotics, hygromycin A (HygA) and macrolides, which target peptidyl transferase center and peptide exit tunnel, respectively, can act cooperatively against susceptible and drug-resistant bacteria. Remarkably, HygA slows down macrolide dissociation from the ribosome by 60-fold and enhances the otherwise weak antimicrobial activity of the newest-generation macrolide drugs known as ketolides against macrolide-resistant bacteria. By determining a set of high-resolution X-ray crystal structures of drug-sensitive wild-type and macrolide-resistant Erm-methylated 70S ribosomes in complex with three HygA-macrolide pairs, we provide a structural rationale for the binding cooperativity of these drugs and also uncover the molecular mechanism of overcoming Erm-type resistance by macrolides acting together with hygromycin A. Altogether our structural, biochemical, and microbiological findings lay the foundation for the subsequent development of synergistic antibiotic tandems with improved bactericidal properties against drug-resistant pathogens, including those expressing erm genes.

			Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A.,Chen CW, Leimer N, Syroegin EA, Dunand C, Bulman ZP, Lewis K, Polikanov YS, Svetlov MS Nat Commun. 2023 Jul 14;14(1):4196. doi: 10.1038/s41467-023-39653-5. PMID:37452045<ref>PMID:37452045</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 8fc2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]		*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:34, 15 November 2023

2023-11-15T11:34:49Z

← Older revision		Revision as of 11:34, 15 November 2023
Line 13:		Line 13:
	==See Also==		==See Also==
	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]		*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
			*[[Ribosome 3D structures\|Ribosome 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:32, 25 October 2023

2023-10-25T10:32:16Z

← Older revision		Revision as of 10:32, 25 October 2023
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RL3_THET8 RL3_THET8] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_B]		[https://www.uniprot.org/uniprot/RL3_THET8 RL3_THET8] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_B]

			==See Also==
			*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:20, 12 July 2023

2023-07-12T07:20:27Z

← Older revision		Revision as of 07:20, 12 July 2023
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry 8fc2 is ON HOLD~~		==Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.50A resolution==
			<StructureSection load='8fc2' size='340' side='right'caption='[[8fc2]], [[Resolution\|resolution]] 2.50Å' scene=''>
	~~Authors: Chen, C.-W., Syroegin, E.A., Svetlov, M.S., Polikanov, Y.S.~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[8fc2]] 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=8FC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8FC2 FirstGlance]. <br>
	~~Description:~~ Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.50A resolution		</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>
	[[~~Category~~: ~~Unreleased Structures~~]]		<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=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=HGR:HYGROMYCIN+A'>HGR</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=ZIT:AZITHROMYCIN'>ZIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	[[~~Category~~: ~~Polikanov~~, Y.S]]		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8fc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8fc2 OCA], [https://pdbe.org/8fc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8fc2 RCSB], [https://www.ebi.ac.uk/pdbsum/8fc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8fc2 ProSAT]</span></td></tr>
	[[~~Category~~: ~~Syroegin~~, E.A]]		</table>
	[[Category: Chen, C.-W]]		== Function ==
	[[Category: Svetlov~~, M.S~~]]		[https://www.uniprot.org/uniprot/RL3_THET8 RL3_THET8] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_B]
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Thermus thermophilus HB8]]
			[[Category: Chen C-W]]
			[[Category: Polikanov YS]]
			[[Category: Svetlov MS]]
			[[Category: Syroegin EA]]

OCA: Protected "8fc2" [edit=sysop:move=sysop]

2022-12-07T05:42:16Z

Protected "8fc2" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:42, 7 December 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8fc2 is ON HOLD Authors: Chen, C.-W., Syroegin, E.A., Svetlov, M.S., Polikanov, Y.S. Description: Crystal structure of the Thermus thermophilus 70S...

2022-12-07T05:42:14Z

New page: '''Unreleased structure''' The entry 8fc2 is ON HOLD Authors: Chen, C.-W., Syroegin, E.A., Svetlov, M.S., Polikanov, Y.S. Description: Crystal structure of the Thermus thermophilus 70S...

New page

'''Unreleased structure'''

The entry 8fc2 is ON HOLD

Authors: Chen, C.-W., Syroegin, E.A., Svetlov, M.S., Polikanov, Y.S.

Description: Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.50A resolution
[[Category: Unreleased Structures]]
[[Category: Polikanov, Y.S]]
[[Category: Syroegin, E.A]]
[[Category: Chen, C.-W]]
[[Category: Svetlov, M.S]]