7jql - Revision history

OCA at 10:57, 15 November 2023

2023-11-15T10:57:31Z

←Older revision		Revision as of 10:57, 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 15:09, 18 October 2023

2023-10-18T15:09:27Z

←Older revision		Revision as of 15:09, 18 October 2023
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-	====	+	==Crystal structure of the Thermus thermophilus 70S ribosome in complex with Bac7-001, mRNA, and deacylated P-site tRNA at 3.00A resolution==
-	<StructureSection load='7jql' size='340' side='right'caption='[[7jql]]' scene=''>	+	<StructureSection load='7jql' size='340' side='right'caption='[[7jql]], [[Resolution\|resolution]] 3.00Å' 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'>[[7jql]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus], [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] and [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=7JQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JQL 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=7jql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jql OCA], [~~http~~://pdbe.org/7jql PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jql RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jql PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jql 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]] 3Å</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=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=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=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=7jql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jql OCA], [https://pdbe.org/7jql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jql RCSB], [https://www.ebi.ac.uk/pdbsum/7jql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jql ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proline-rich antimicrobial peptides (PrAMPs) are promising lead compounds for developing new antimicrobials; however, their narrow spectrum of action is limiting. PrAMPs kill bacteria binding to their ribosomes and inhibiting protein synthesis. In this study, 133 derivatives of the PrAMP Bac7(1-16) were synthesized to identify the crucial residues for ribosome inactivation and antimicrobial activity. Then, five new Bac7(1-16) derivatives were conceived and characterized by antibacterial and membrane permeabilization assays, X-ray crystallography, and molecular dynamics simulations. Some derivatives displayed broad spectrum activity, encompassing Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Staphylococcus aureus. Two peptides out of five acquired a weak membrane-perturbing activity while maintaining the ability to inhibit protein synthesis. These derivatives became independent of the SbmA transporter, commonly used by native PrAMPs, suggesting that they obtained a novel route to enter bacterial cells. PrAMP-derived compounds could become new-generation antimicrobials to combat antibiotic-resistant pathogens.
		+
		+	Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens.,Mardirossian M, Sola R, Beckert B, Valencic E, Collis DWP, Borisek J, Armas F, Di Stasi A, Buchmann J, Syroegin EA, Polikanov YS, Magistrato A, Hilpert K, Wilson DN, Scocchi M J Med Chem. 2020 Aug 13. doi: 10.1021/acs.jmedchem.0c00665. PMID:32787108<ref>PMID:32787108</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jql" 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: Bos taurus]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Thermus thermophilus HB8]]
		+	[[Category: Armas F]]
		+	[[Category: Beckert B]]
		+	[[Category: Borisek J]]
		+	[[Category: Buchmann J]]
		+	[[Category: Collis DWP]]
		+	[[Category: Di Stasi A]]
		+	[[Category: Hilpert K]]
		+	[[Category: Magistrato A]]
		+	[[Category: Mardirossian M]]
		+	[[Category: Polikanov YS]]
		+	[[Category: Scocchi M]]
		+	[[Category: Sola R]]
		+	[[Category: Syroegin EA]]
		+	[[Category: Valencic E]]
		+	[[Category: Wilson DN]]

OCA at 11:20, 26 August 2020

2020-08-26T11:20:34Z

←Older revision		Revision as of 11:20, 26 August 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7jql ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7jql' size='340' side='right'caption='[[7jql]]' scene=''>
-	~~Authors~~: ~~Mardirossian, M~~.~~, Sola, R~~.~~, Beckert, B~~.~~, Valencic, E~~.~~, Collis, D.W.P., Borisek, J., Armas, F., Di Stasi, A., Buchmann, J., Syroegin, E.A., Polikanov, Y.S., Magistrato, A., Hilpert, K., Wilson, D.N., Scocchi, M.~~	+	== 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 Thermus thermophilus 70S ribosome in complex with Bac7-001, mRNA, and deacylated P-site tRNA at 3.00A 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=7jql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jql OCA], [http://pdbe.org/7jql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jql RCSB], [http://www.ebi.ac.uk/pdbsum/7jql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jql ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures]~~]	+	</table>
-	~~[[Category~~: ~~Magistrato, A]]~~	+	__TOC__
-	[~~[Category~~: ~~Polikanov, Y~~.S]]	+	</StructureSection>
-	~~[[Category: Beckert~~, ~~B]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Buchmann, J~~]]	+	[[Category: Z-disk]]
-	~~[[Category: Valencic~~, ~~E]]~~	+
-	[~~[Category~~: ~~Syroegin, E~~.A]]	+
-	~~[[Category: Di Stasi~~, ~~A]]~~	+
-	[~~[Category~~: ~~Hilpert, K~~]]	+
-	~~[[Category: Mardirossian~~, ~~M]]~~	+
-	[~~[Category~~: ~~Wilson, D~~.N]]	+
-	[~~[Category~~: ~~Collis, D~~.W.P]]	+
-	~~[[Category: Armas, F]]~~	+
-	~~[[Category: Scocchi, M]]~~	+
-	[[Category: ~~Sola, R~~]]	+
-	[[Category: ~~Borisek, J~~]]	+

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

2020-08-19T04:54:33Z

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

←Older revision

Revision as of 04:54, 19 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jql is ON HOLD Authors: Mardirossian, M., Sola, R., Beckert, B., Valencic, E., Collis, D.W.P., Borisek, J., Armas, F., Di Stasi, A., Buchmann, J., ...

2020-08-19T04:54:32Z

New page: '''Unreleased structure''' The entry 7jql is ON HOLD Authors: Mardirossian, M., Sola, R., Beckert, B., Valencic, E., Collis, D.W.P., Borisek, J., Armas, F., Di Stasi, A., Buchmann, J., ...

New page

'''Unreleased structure'''

The entry 7jql is ON HOLD

Authors: Mardirossian, M., Sola, R., Beckert, B., Valencic, E., Collis, D.W.P., Borisek, J., Armas, F., Di Stasi, A., Buchmann, J., Syroegin, E.A., Polikanov, Y.S., Magistrato, A., Hilpert, K., Wilson, D.N., Scocchi, M.

Description: Crystal structure of the Thermus thermophilus 70S ribosome in complex with Bac7-001, mRNA, and deacylated P-site tRNA at 3.00A resolution
[[Category: Unreleased Structures]]
[[Category: Magistrato, A]]
[[Category: Polikanov, Y.S]]
[[Category: Beckert, B]]
[[Category: Buchmann, J]]
[[Category: Valencic, E]]
[[Category: Syroegin, E.A]]
[[Category: Di Stasi, A]]
[[Category: Hilpert, K]]
[[Category: Mardirossian, M]]
[[Category: Wilson, D.N]]
[[Category: Collis, D.W.P]]
[[Category: Armas, F]]
[[Category: Scocchi, M]]
[[Category: Sola, R]]
[[Category: Borisek, J]]