7jqm - Revision history

OCA at 10:57, 15 November 2023

OCA — Wed, 15 Nov 2023 10:57:36 GMT

←Older revision		Revision as of 10:57, 15 November 2023
Line 21:		Line 21:

	==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

OCA — Wed, 18 Oct 2023 15:09:29 GMT

←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 Bac7-002, mRNA, and deacylated P-site tRNA at 3.05A resolution==
-	<StructureSection load='7jqm' size='340' side='right'caption='[[7jqm]]' scene=''>	+	<StructureSection load='7jqm' size='340' side='right'caption='[[7jqm]], [[Resolution\|resolution]] 3.05Å' 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'>[[7jqm]] 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=7JQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JQM 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=7jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jqm OCA], [~~http~~://pdbe.org/7jqm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jqm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jqm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jqm 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]] 3.05Å</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=7jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jqm OCA], [https://pdbe.org/7jqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jqm RCSB], [https://www.ebi.ac.uk/pdbsum/7jqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jqm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_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 7jqm" 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: 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

OCA — Wed, 26 Aug 2020 11:20:36 GMT

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

-	~~The entry~~ 7jqm ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7jqm' size='340' side='right'caption='[[7jqm]]' 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 Bac7-002, mRNA, and deacylated P-site tRNA at 3.05A 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=7jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jqm OCA], [http://pdbe.org/7jqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jqm RCSB], [http://www.ebi.ac.uk/pdbsum/7jqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jqm 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 "7jqm" [edit=sysop:move=sysop]

OCA — Wed, 19 Aug 2020 04:55:06 GMT

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

←Older revision

Revision as of 04:55, 19 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jqm 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., ...

OCA — Wed, 19 Aug 2020 04:55:04 GMT

New page: '''Unreleased structure''' The entry 7jqm 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 7jqm 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 Bac7-002, mRNA, and deacylated P-site tRNA at 3.05A 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]]