4wao - Revision history

OCA: Redirecting to 4wf1

OCA — Wed, 10 Dec 2014 15:58:40 GMT

Redirecting to 4wf1

←Older revision		Revision as of 15:58, 10 December 2014
Line 1:		Line 1:
-	~~==Crystal structure of the E. coli ribosome bound to negamycin. This file contains the 30S subunit of the first 70S ribosome.==~~	+	#REDIRECT [[4wf1]] This PDB entry is obsolete and replaced by 4wf1
-	~~<StructureSection load='4wao' size='340' side='right' caption='~~[[~~4wao]], [[Resolution\|resolution]] 3.09Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[4wao~~]] is ~~a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]~~ and [http://en.wikipedia.org/wiki/Escherichia_coli_str._k-12_substr._mg1655 Escherichia coli str. k-12 substr. mg1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WAO FirstGlance]. <br>	+
-	~~</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>~~	+
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wap\|4wap]], [[4waq\|4waq]], [[4war\|4war]]</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=4wao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wao OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wao RCSB], [http://www.ebi.ac.uk/pdbsum/4wao PDBsum]</span></td></tr>	+
-	~~</table>~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 A resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation.	+
-		+
-	Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.,Olivier NB, Altman RB, Noeske J, Basarab GS, Code E, Ferguson AD, Gao N, Huang J, Juette MF, Livchak S, Miller MD, Prince DB, Cate JH, Buurman ET, Blanchard SC Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201414401. PMID:25368144<ref>PMID:25368144</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Escherichia coli]]~~	+
-	~~[[Category: Escherichia coli str. k-12 substr. mg1655]]~~	+
-	~~[[Category: Altman, R B]]~~	+
-	~~[[Category: Basarab, G S]]~~	+
-	~~[[Category: Blanchard, S C]]~~	+
-	~~[[Category: Buurman, E T]]~~	+
-	~~[[Category: Cate, J H.D]]~~	+
-	~~[[Category: Code, E]]~~	+
-	~~[[Category: Ferguson, A D]]~~	+
-	~~[[Category: Gao, N]]~~	+
-	~~[[Category: Huang, J]]~~	+
-	~~[[Category: Juette, M F]]~~	+
-	~~[[Category: Livchak, S]]~~	+
-	~~[[Category: Miller, M D]]~~	+
-	~~[[Category: Noeske, J]]~~	+
-	~~[[Category: Olivier, N B]]~~	+
-	~~[[Category: Prince, D B]]~~	+
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Exit]]~~	+
-	~~[[Category: Peptidyl]]~~	+
-	~~[[Category: Protein biosynthesis]]~~	+
-	~~[[Category: Ribosomal subunit]]~~	+
-	~~[[Category: Ribosome-antibiotic complex]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Streptogramin]]~~	+
-	~~[[Category: Transfer]]~~	+

OCA at 10:52, 19 November 2014

OCA — Wed, 19 Nov 2014 10:52:54 GMT

←Older revision		Revision as of 10:52, 19 November 2014
Line 7:		Line 7:
	<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=4wao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wao OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wao RCSB], [http://www.ebi.ac.uk/pdbsum/4wao PDBsum]</span></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=4wao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wao OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wao RCSB], [http://www.ebi.ac.uk/pdbsum/4wao PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 A resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation.
		+
		+	Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.,Olivier NB, Altman RB, Noeske J, Basarab GS, Code E, Ferguson AD, Gao N, Huang J, Juette MF, Livchak S, Miller MD, Prince DB, Cate JH, Buurman ET, Blanchard SC Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201414401. PMID:25368144<ref>PMID:25368144</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Escherichia coli str. k-12 substr. mg1655]]		[[Category: Escherichia coli str. k-12 substr. mg1655]]
-	[[Category: Altman, R B.]]	+	[[Category: Altman, R B]]
-	[[Category: Basarab, G S.]]	+	[[Category: Basarab, G S]]
-	[[Category: Blanchard, S C.]]	+	[[Category: Blanchard, S C]]
-	[[Category: Buurman, E T.]]	+	[[Category: Buurman, E T]]
-	[[Category: Cate, J H.D.]]	+	[[Category: Cate, J H.D]]
-	[[Category: Code, E.]]	+	[[Category: Code, E]]
-	[[Category: Ferguson, A D.]]	+	[[Category: Ferguson, A D]]
-	[[Category: Gao, N.]]	+	[[Category: Gao, N]]
-	[[Category: Huang, J.]]	+	[[Category: Huang, J]]
-	[[Category: Juette, M F.]]	+	[[Category: Juette, M F]]
-	[[Category: Livchak, S.]]	+	[[Category: Livchak, S]]
-	[[Category: Miller, M D.]]	+	[[Category: Miller, M D]]
-	[[Category: Noeske, J.]]	+	[[Category: Noeske, J]]
-	[[Category: Olivier, N B.]]	+	[[Category: Olivier, N B]]
-	[[Category: Prince, D B~~.]]~~	+	[[Category: Prince, D B]]
-	~~[[Category: 16]]~~	+
-	~~[[Category: 30]]~~	+
-	~~[[Category: 70~~]]	+
	[[Category: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Exit]]		[[Category: Exit]]

OCA at 09:05, 5 November 2014

OCA — Wed, 05 Nov 2014 09:05:22 GMT

←Older revision		Revision as of 09:05, 5 November 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of the E. coli ribosome bound to negamycin. This file contains the 30S subunit of the first 70S ribosome.==
-		+	<StructureSection load='4wao' size='340' side='right' caption='[[4wao]], [[Resolution\|resolution]] 3.09Å' scene=''>
-	~~The entry~~ 4wao is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4wao]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Escherichia_coli_str._k-12_substr._mg1655 Escherichia coli str. k-12 substr. mg1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WAO FirstGlance]. <br>
-	~~Authors~~: ~~Olivier~~, N.B., ~~Altman~~, R.B., ~~Noeske, J~~., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak, S., Miller, M.D., ~~Prince, D~~.B., ~~Cate, J.H.~~D.~~, Buurman, E.T., Blanchard, S.C., Blanchard, S.C.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4wap\|4wap]], [[4waq\|4waq]], [[4war\|4war]]</td></tr>
-	~~Description~~: ~~Crystal structure of the E. coli ribosome bound to negamycin. This file contains the 30S~~ subunit ~~of the first 70S ribosome.~~	+	<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=4wao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wao OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wao RCSB], [http://www.ebi.ac.uk/pdbsum/4wao PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Escherichia coli str. k-12 substr. mg1655]]
		+	[[Category: Altman, R B.]]
		+	[[Category: Basarab, G S.]]
		+	[[Category: Blanchard, S C.]]
		+	[[Category: Buurman, E T.]]
		+	[[Category: Cate, J H.D.]]
		+	[[Category: Code, E.]]
		+	[[Category: Ferguson, A D.]]
		+	[[Category: Gao, N.]]
		+	[[Category: Huang, J.]]
		+	[[Category: Juette, M F.]]
		+	[[Category: Livchak, S.]]
		+	[[Category: Miller, M D.]]
		+	[[Category: Noeske, J.]]
		+	[[Category: Olivier, N B.]]
		+	[[Category: Prince, D B.]]
		+	[[Category: 16]]
		+	[[Category: 30]]
		+	[[Category: 70]]
		+	[[Category: Antibiotic]]
		+	[[Category: Exit]]
		+	[[Category: Peptidyl]]
		+	[[Category: Protein biosynthesis]]
		+	[[Category: Ribosomal subunit]]
		+	[[Category: Ribosome-antibiotic complex]]
		+	[[Category: Ribosome]]
		+	[[Category: Rna]]
		+	[[Category: Streptogramin]]
		+	[[Category: Transfer]]

OCA at 09:05, 24 September 2014

OCA — Wed, 24 Sep 2014 09:05:46 GMT

←Older revision		Revision as of 09:05, 24 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4wao is ON HOLD	+	The entry 4wao is ON HOLD until Paper Publication

	Authors: Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak, S., Miller, M.D., Prince, D.B., Cate, J.H.D., Buurman, E.T., Blanchard, S.C., Blanchard, S.C.		Authors: Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak, S., Miller, M.D., Prince, D.B., Cate, J.H.D., Buurman, E.T., Blanchard, S.C., Blanchard, S.C.

	Description: Crystal structure of the E. coli ribosome bound to negamycin. This file contains the 30S subunit of the first 70S ribosome.		Description: Crystal structure of the E. coli ribosome bound to negamycin. This file contains the 30S subunit of the first 70S ribosome.

OCA: Protected "4wao" [edit=sysop:move=sysop]

OCA — Wed, 10 Sep 2014 08:53:56 GMT

Protected "4wao" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:53, 10 September 2014

OCA: New page: '''Unreleased structure''' The entry 4wao is ON HOLD Authors: Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak...

OCA — Wed, 10 Sep 2014 08:53:54 GMT

New page: '''Unreleased structure''' The entry 4wao is ON HOLD Authors: Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak...

New page

'''Unreleased structure'''

The entry 4wao is ON HOLD

Authors: Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak, S., Miller, M.D., Prince, D.B., Cate, J.H.D., Buurman, E.T., Blanchard, S.C., Blanchard, S.C.

Description: Crystal structure of the E. coli ribosome bound to negamycin. This file contains the 30S subunit of the first 70S ribosome.