5zej - Revision history

OCA at 08:52, 22 November 2023

OCA — Wed, 22 Nov 2023 08:52:33 GMT

←Older revision		Revision as of 08:52, 22 November 2023
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	<StructureSection load='5zej' size='340' side='right'caption='[[5zej]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5zej' size='340' side='right'caption='[[5zej]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zej]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4wcr 4wcr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZEJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zej]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4wcr 4wcr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZEJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>~~</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]] 3.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5zeg\|5zeg]], [[5zei\|5zei]]~~</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=5zej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zej OCA], [https://pdbe.org/5zej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zej RCSB], [https://www.ebi.ac.uk/pdbsum/5zej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zej ProSAT]</span></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=5zej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zej OCA], [~~http~~://pdbe.org/5zej PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zej RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zej PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zej ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baba, F]]	+	[[Category: Synthetic construct]]
-	[[Category: Kanazawa, H]]	+	[[Category: Baba F]]
-	[[Category: Koganei, M]]	+	[[Category: Kanazawa H]]
-	[[Category: Kondo, J]]	+	[[Category: Koganei M]]
-	~~[[Category: Aminoglycoside]]~~	+	[[Category: Kondo J]]
-	~~[[Category: Antibiotic-resistance]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 21:18, 28 October 2020

OCA — Wed, 28 Oct 2020 21:18:56 GMT

←Older revision		Revision as of 21:18, 28 October 2020
Line 1:		Line 1:

	==Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin==		==Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin==
-	<StructureSection load='5zej' size='340' side='right' caption='[[5zej]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5zej' size='340' side='right'caption='[[5zej]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zej]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZEJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zej]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4wcr 4wcr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZEJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zeg\|5zeg]], [[5zei\|5zei]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zeg\|5zeg]], [[5zei\|5zei]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5zej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zej OCA], [http://pdbe.org/5zej PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zej RCSB], [http://www.ebi.ac.uk/pdbsum/5zej PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zej ProSAT]</span></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=5zej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zej OCA], [http://pdbe.org/5zej PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zej RCSB], [http://www.ebi.ac.uk/pdbsum/5zej PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zej ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baba, F]]		[[Category: Baba, F]]
	[[Category: Kanazawa, H]]		[[Category: Kanazawa, H]]

OCA at 07:36, 21 March 2018

OCA — Wed, 21 Mar 2018 07:36:57 GMT

←Older revision		Revision as of 07:36, 21 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5zej is ~~ON HOLD~~	+	==Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin==
		+	<StructureSection load='5zej' size='340' side='right' caption='[[5zej]], [[Resolution\|resolution]] 3.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zej]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZEJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zeg\|5zeg]], [[5zei\|5zei]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zej OCA], [http://pdbe.org/5zej PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zej RCSB], [http://www.ebi.ac.uk/pdbsum/5zej PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zej ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The aminoglycoside resistance conferred by an N1-methylation of A1408 in 16S rRNA by a novel plasmid-mediated methyltransferase NpmA can be a future health threat. In the present study, we have determined crystal structures of the bacterial ribosomal decoding A site with an A1408m1A antibiotic-resistance mutation both in the presence and absence of aminoglycosides. G418 and paromomycin both possessing a 6'-OH group specifically bind to the mutant A site and disturb its function as a molecular switch in the decoding process. On the other hand, binding of gentamicin with a 6'-NH3+ group to the mutant A site could not be observed in the present crystal structure. These observations agree with the minimum inhibitory concentration of aminoglycosides against Escherichia coli. In addition, one of our crystal structures suggests a possible conformational change of A1408 during the N1-methylation reaction by NpmA. The structural information obtained explains how bacteria acquire resistance against aminoglycosides along with a minimum of fitness cost by the N1-methylation of A1408 and provides novel information for designing the next-generation aminoglycoside.

-	~~Authors: Kanazawa~~, H., Baba, F., Koganei, M., Kondo, J.	+	A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.,Kanazawa H, Baba F, Koganei M, Kondo J Nucleic Acids Res. 2017 Dec 1;45(21):12529-12535. doi: 10.1093/nar/gkx882. PMID:29036479<ref>PMID:29036479</ref>

-	~~Description: Crystal structure~~ of the ~~bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Kondo, J]]~~	+	<div class="pdbe-citations 5zej" style="background-color:#fffaf0;"></div>
-	~~[[Category: Koganei, M]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Baba, F]]		[[Category: Baba, F]]
	[[Category: Kanazawa, H]]		[[Category: Kanazawa, H]]
		+	[[Category: Koganei, M]]
		+	[[Category: Kondo, J]]
		+	[[Category: Aminoglycoside]]
		+	[[Category: Antibiotic-resistance]]
		+	[[Category: Ribosome]]
		+	[[Category: Rna]]

OCA at 04:59, 14 March 2018

OCA — Wed, 14 Mar 2018 04:59:24 GMT

←Older revision		Revision as of 04:59, 14 March 2018
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	Authors: Kanazawa, H., Baba, F., Koganei, M., Kondo, J.		Authors: Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

-	Description: Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site	+	Description: Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kondo, J]]		[[Category: Kondo, J]]

OCA: Protected "5zej" [edit=sysop:move=sysop]

OCA — Thu, 08 Mar 2018 03:38:53 GMT

Protected "5zej" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:38, 8 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zej is ON HOLD Authors: Kanazawa, H., Baba, F., Koganei, M., Kondo, J. Description: Crystal structure of the bacterial A1408me1A-mutant ribosomal ...

OCA — Thu, 08 Mar 2018 03:38:51 GMT

New page: '''Unreleased structure''' The entry 5zej is ON HOLD Authors: Kanazawa, H., Baba, F., Koganei, M., Kondo, J. Description: Crystal structure of the bacterial A1408me1A-mutant ribosomal ...

New page

'''Unreleased structure'''

The entry 5zej is ON HOLD

Authors: Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Description: Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site
[[Category: Unreleased Structures]]
[[Category: Kondo, J]]
[[Category: Koganei, M]]
[[Category: Baba, F]]
[[Category: Kanazawa, H]]