2qb9 - Revision history

OCA: Redirecting to 4v53

2014-12-10T15:12:30Z

Redirecting to 4v53

←Older revision		Revision as of 15:12, 10 December 2014
Line 1:		Line 1:
-	==Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.==	+	#REDIRECT [[4v53]] This PDB entry is obsolete and replaced by 4v53
-	~~<StructureSection load='2qb9' size='340' side='right' caption='~~[[~~2qb9]], [[Resolution\|resolution]] 3.54Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[2qb9~~]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QB9 FirstGlance]. <br>	+
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+
-	~~<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qba\|2qba]], [[2qbb\|2qbb]], [[2qbc\|2qbc]]</td></tr>~~	+
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qb9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qb9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qb9 PDBsum]</span></td></tr>	+
-	~~<table>~~	+
-	~~== Evolutionary Conservation ==~~	+
-	~~[[Image:Consurf_key_small.gif\|200px\|right]]~~	+
-	~~Check<jmol>~~	+
-	~~<jmolCheckbox>~~	+
-	~~<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/2qb9_consurf.spt"</scriptWhenChecked>~~	+
-	~~<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>~~	+
-	~~<text>to colour the structure by Evolutionary Conservation</text>~~	+
-	~~</jmolCheckbox>~~	+
-	~~</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method~~ and ~~the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].~~	+
-	~~<div style="clear:both"></div>~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Aminoglycosides are widely used antibiotics that cause messenger RNA decoding errors, block mRNA and transfer RNA translocation, and inhibit ribosome recycling. Ribosome recycling follows the termination of protein synthesis and is aided by ribosome recycling factor (RRF) in bacteria. The molecular mechanism by which aminoglycosides inhibit ribosome recycling is unknown. Here we show in X-ray crystal structures of the Escherichia coli 70S ribosome that RRF binding causes RNA helix H69 of the large ribosomal subunit, which is crucial for subunit association, to swing away from the subunit interface. Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling.	+
-		+
-	Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.,Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH Nat Struct Mol Biol. 2007 Aug;14(8):727-32. Epub 2007 Jul 29. PMID:17660832<ref>PMID:17660832</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-		+
-	~~==See Also==~~	+
-	*[[Ribosomal protein THX\|Ribosomal protein THX]]	+
-	*[[Ribosome 3D structures\|Ribosome 3D structures]]	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Escherichia coli]]~~	+
-	~~[[Category: Borovinskaya, M A.]]~~	+
-	~~[[Category: Cate, J H.D.]]~~	+
-	~~[[Category: Hirokawa, G.]]~~	+
-	~~[[Category: Holton, J M.]]~~	+
-	~~[[Category: Kaji, A.]]~~	+
-	~~[[Category: Kaji, H.]]~~	+
-	~~[[Category: Pai, R D.]]~~	+
-	~~[[Category: Schuwirth, B S.]]~~	+
-	~~[[Category: Zhang, W.]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Rna-protein complex]]~~	+

OCA at 06:56, 29 September 2014

2014-09-29T06:56:14Z

←Older revision		Revision as of 06:56, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qb9.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.==
		+	<StructureSection load='2qb9' size='340' side='right' caption='[[2qb9]], [[Resolution\|resolution]] 3.54Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qb9]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QB9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qba\|2qba]], [[2qbb\|2qbb]], [[2qbc\|2qbc]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qb9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qb9 RCSB], [http://www.ebi.ac.uk/pdbsum/2qb9 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/2qb9_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aminoglycosides are widely used antibiotics that cause messenger RNA decoding errors, block mRNA and transfer RNA translocation, and inhibit ribosome recycling. Ribosome recycling follows the termination of protein synthesis and is aided by ribosome recycling factor (RRF) in bacteria. The molecular mechanism by which aminoglycosides inhibit ribosome recycling is unknown. Here we show in X-ray crystal structures of the Escherichia coli 70S ribosome that RRF binding causes RNA helix H69 of the large ribosomal subunit, which is crucial for subunit association, to swing away from the subunit interface. Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling.

-	~~{{STRUCTURE_2qb9\| PDB=2qb9 \| SCENE= }}~~	+	Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.,Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH Nat Struct Mol Biol. 2007 Aug;14(8):727-32. Epub 2007 Jul 29. PMID:17660832<ref>PMID:17660832</ref>

-	~~===Crystal structure~~ of the ~~bacterial ribosome from Escherichia coli in complex with gentamicin~~. ~~This file contains the 30S subunit~~ of ~~the first 70S ribosome, with gentamicin bound~~. ~~The entire crystal structure contains two 70S ribosomes and is described in remark 400.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17660832}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2qb9]] is a 21 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].~~	+

	==See Also==		==See Also==
-	*[[Ribosomal protein S10\|Ribosomal protein S10]]
-	*[[Ribosomal protein S11\|Ribosomal protein S11]]
-	*[[Ribosomal protein S12\|Ribosomal protein S12]]
-	*[[Ribosomal protein S13\|Ribosomal protein S13]]
-	*[[Ribosomal protein S14\|Ribosomal protein S14]]
-	*[[Ribosomal protein S15\|Ribosomal protein S15]]
-	*[[Ribosomal protein S16\|Ribosomal protein S16]]
-	*[[Ribosomal protein S17\|Ribosomal protein S17]]
-	*[[Ribosomal protein S18\|Ribosomal protein S18]]
-	*[[Ribosomal protein S19\|Ribosomal protein S19]]
-	*[[Ribosomal protein S2\|Ribosomal protein S2]]
-	*[[Ribosomal protein S20\|Ribosomal protein S20]]
-	*[[Ribosomal protein S21\|Ribosomal protein S21]]
-	*[[Ribosomal protein S3\|Ribosomal protein S3]]
-	*[[Ribosomal protein S4\|Ribosomal protein S4]]
-	*[[Ribosomal protein S5\|Ribosomal protein S5]]
-	*[[Ribosomal protein S6\|Ribosomal protein S6]]
-	*[[Ribosomal protein S7\|Ribosomal protein S7]]
-	*[[Ribosomal protein S8\|Ribosomal protein S8]]
-	*[[Ribosomal protein S9\|Ribosomal protein S9]]
	*[[Ribosomal protein THX\|Ribosomal protein THX]]		*[[Ribosomal protein THX\|Ribosomal protein THX]]
-	*[[Ribosome\|Ribosome]]	+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017660832<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Borovinskaya, M A.]]		[[Category: Borovinskaya, M A.]]

OCA at 12:57, 20 October 2012

2012-10-20T12:57:51Z

←Older revision		Revision as of 12:57, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2qb9]] is a 21 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S14]], [[Ribosomal protein S15]], [[Ribosomal protein S16]], [[Ribosomal protein S17]], [[Ribosomal protein S18]], [[Ribosomal protein S19]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S21]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein S5]], [[Ribosomal protein S6]], [[Ribosomal protein S7]], [[Ribosomal protein S8]], [[Ribosomal protein S9]], [[Ribosomal protein THX]] and [[Ribosome]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].	+	[[2qb9]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].

	==See Also==		==See Also==

OCA at 10:30, 26 July 2012

2012-07-26T10:30:31Z

←Older revision		Revision as of 10:30, 26 July 2012
Line 1:		Line 1:
	[[Image:2qb9.png\|left\|200px]]		[[Image:2qb9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qb9", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2qb9\| PDB=2qb9 \| SCENE= }}		{{STRUCTURE_2qb9\| PDB=2qb9 \| SCENE= }}

	===Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.===		===Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17660832}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17660832 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17660832}}		{{ABSTRACT_PUBMED_17660832}}

	==About this Structure==		==About this Structure==
-	[[2qb9]] is a 21 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S15]], [[Ribosomal protein S17]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S21]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein THX]] and [[Ribosome]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].	+	[[2qb9]] is a 21 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S14]], [[Ribosomal protein S15]], [[Ribosomal protein S16]], [[Ribosomal protein S17]], [[Ribosomal protein S18]], [[Ribosomal protein S19]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S21]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein S5]], [[Ribosomal protein S6]], [[Ribosomal protein S7]], [[Ribosomal protein S8]], [[Ribosomal protein S9]], [[Ribosomal protein THX]] and [[Ribosome]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].

	==See Also==		==See Also==
-	*[[Ribosomal protein S10]]	+	*[[Ribosomal protein S10\|Ribosomal protein S10]]
-	*[[Ribosomal protein S11]]	+	*[[Ribosomal protein S11\|Ribosomal protein S11]]
-	*[[Ribosomal protein S12]]	+	*[[Ribosomal protein S12\|Ribosomal protein S12]]
-	*[[Ribosomal protein S13]]	+	*[[Ribosomal protein S13\|Ribosomal protein S13]]
-	*[[Ribosomal protein S15]]	+	*[[Ribosomal protein S14\|Ribosomal protein S14]]
-	*[[Ribosomal protein S17]]	+	*[[Ribosomal protein S15\|Ribosomal protein S15]]
-	*[[Ribosomal protein S2]]	+	*[[Ribosomal protein S16\|Ribosomal protein S16]]
-	*[[Ribosomal protein S20]]	+	*[[Ribosomal protein S17\|Ribosomal protein S17]]
-	*[[Ribosomal protein S21]]	+	*[[Ribosomal protein S18\|Ribosomal protein S18]]
-	*[[Ribosomal protein S3]]	+	*[[Ribosomal protein S19\|Ribosomal protein S19]]
-	*[[Ribosomal protein S4]]	+	*[[Ribosomal protein S2\|Ribosomal protein S2]]
-	*[[Ribosomal protein THX]]	+	*[[Ribosomal protein S20\|Ribosomal protein S20]]
-	*[[Ribosome]]	+	*[[Ribosomal protein S21\|Ribosomal protein S21]]
		+	*[[Ribosomal protein S3\|Ribosomal protein S3]]
		+	*[[Ribosomal protein S4\|Ribosomal protein S4]]
		+	*[[Ribosomal protein S5\|Ribosomal protein S5]]
		+	*[[Ribosomal protein S6\|Ribosomal protein S6]]
		+	*[[Ribosomal protein S7\|Ribosomal protein S7]]
		+	*[[Ribosomal protein S8\|Ribosomal protein S8]]
		+	*[[Ribosomal protein S9\|Ribosomal protein S9]]
		+	*[[Ribosomal protein THX\|Ribosomal protein THX]]
		+	*[[Ribosome\|Ribosome]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17660832~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017660832</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Borovinskaya, M A.]]		[[Category: Borovinskaya, M A.]]

OCA: Protected "2qb9" [edit=sysop:move=sysop]

2010-12-27T00:19:37Z

Protected "2qb9" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:19, 27 December 2010

OCA at 00:19, 27 December 2010

2010-12-27T00:19:36Z

←Older revision		Revision as of 00:19, 27 December 2010
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2qb9.png\|left\|200px]]		[[Image:2qb9.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2QB9~~ is a 21 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].	+	[[2qb9]] is a 21 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S15]], [[Ribosomal protein S17]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S21]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein THX]] and [[Ribosome]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].
		+
		+	==See Also==
		+	*[[Ribosomal protein S10]]
		+	*[[Ribosomal protein S11]]
		+	*[[Ribosomal protein S12]]
		+	*[[Ribosomal protein S13]]
		+	*[[Ribosomal protein S15]]
		+	*[[Ribosomal protein S17]]
		+	*[[Ribosomal protein S2]]
		+	*[[Ribosomal protein S20]]
		+	*[[Ribosomal protein S21]]
		+	*[[Ribosomal protein S3]]
		+	*[[Ribosomal protein S4]]
		+	*[[Ribosomal protein THX]]
		+	*[[Ribosome]]

	==Reference==		==Reference==
Line 36:		Line 50:
	[[Category: Ribosome]]		[[Category: Ribosome]]
	[[Category: Rna-protein complex]]		[[Category: Rna-protein complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:13:36 2009''

OCA at 05:13, 17 February 2009

2009-02-17T05:13:39Z

←Older revision		Revision as of 05:13, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2QB9 is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].	+	2QB9 is a 21 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB9 OCA].

	==Reference==		==Reference==
-	Structural basis for aminoglycoside inhibition of bacterial ribosome recycling., Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH, Nat Struct Mol Biol. 2007 Aug;14(8):727-32. Epub 2007 Jul 29. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17660832 17660832]~~	+	<ref group="xtra">PMID:17660832</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Protein complex]]
	[[Category: Borovinskaya, M A.]]		[[Category: Borovinskaya, M A.]]
	[[Category: Cate, J H.D.]]		[[Category: Cate, J H.D.]]
Line 38:		Line 37:
	[[Category: Rna-protein complex]]		[[Category: Rna-protein complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 10~~:53:~~40 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:13:36 2009''

OCA at 07:53, 28 July 2008

2008-07-28T07:53:49Z

←Older revision		Revision as of 07:53, 28 July 2008
Line 1:		Line 1:
-	[[Image:2qb9.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2qb9.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2qb9\| PDB=2qb9 \| SCENE= }}		{{STRUCTURE_2qb9\| PDB=2qb9 \| SCENE= }}

-	~~'''~~Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.~~'''~~	+	===Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.===


-	~~==Overview==~~	+	<!--
-	~~Aminoglycosides are widely used antibiotics that cause messenger RNA decoding errors~~, ~~block mRNA and transfer RNA translocation~~, ~~and inhibit ribosome recycling. Ribosome recycling follows~~ the ~~termination of protein synthesis and is aided by ribosome recycling factor~~ (~~RRF) in bacteria~~. ~~The molecular mechanism by which aminoglycosides inhibit ribosome recycling is unknown~~. ~~Here we show in X-ray crystal structures of the Escherichia coli 70S ribosome that RRF binding causes RNA helix H69 of the large ribosomal subunit~~, ~~which~~ is ~~crucial for subunit association, to swing away from~~ the subunit interface. Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17660832}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17660832 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17660832}}

	==About this Structure==		==About this Structure==
Line 33:		Line 37:
	[[Category: Ribosome]]		[[Category: Ribosome]]
	[[Category: Rna-protein complex]]		[[Category: Rna-protein complex]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 14~~:39:55 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 10:53:40 2008''

OCA at 11:39, 4 May 2008

2008-05-04T11:39:56Z

←Older revision		Revision as of 11:39, 4 May 2008
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	[[Image:2qb9.jpg\|left\|200px]]		[[Image:2qb9.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 2qb9 \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>2qb9</scene>, resolution 3.54Å~~	+	The line below this paragraph, containing "STRUCTURE_2qb9", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=A:ADENOSINE~~-~~5'~~-~~MONOPHOSPHATE'>A</scene>~~, ~~<scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>~~, ~~<scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=LLL:~~(~~2R,3R,4R,5R~~)~~-2-~~(~~(1S,2S,3R,4S,6R~~)-4,6-~~DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5~~-~~DIOL'>LLL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene~~>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_2qb9\| PDB=2qb9 \| SCENE= }}
-	~~\|RELATEDENTRY=[[2qba\|2QBA]], [[2qbb\|2QBB]], [[2qbc\|2QBC]]~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qb9 OCA], [http://www.ebi.ac.uk/pdbsum/2qb9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qb9 RCSB]</span>	+
-	}}	+

	'''Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.'''		'''Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400.'''
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	[[Category: Schuwirth, B S.]]		[[Category: Schuwirth, B S.]]
	[[Category: Zhang, W.]]		[[Category: Zhang, W.]]
-	[[Category: ~~ribosome~~]]	+	[[Category: Ribosome]]
-	[[Category: ~~rna~~-protein complex]]	+	[[Category: Rna-protein complex]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 14:39:55 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 04~~:47:09 2008''	+

OCA at 01:47, 31 March 2008

2008-03-31T01:47:12Z

←Older revision		Revision as of 01:47, 31 March 2008
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	\|PDB= 2qb9 \|SIZE=350\|CAPTION= <scene name='initialview01'>2qb9</scene>, resolution 3.54Å		\|PDB= 2qb9 \|SIZE=350\|CAPTION= <scene name='initialview01'>2qb9</scene>, resolution 3.54Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=MG:~~MAGNESIUM+ION~~'>MG</scene> ~~and~~ <scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</scene>	+	\|LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=[[2qba\|2QBA]], [[2qbb\|2QBB]], [[2qbc\|2QBC]]
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qb9 OCA], [http://www.ebi.ac.uk/pdbsum/2qb9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qb9 RCSB]</span>
	}}		}}

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	[[Category: Schuwirth, B S.]]		[[Category: Schuwirth, B S.]]
	[[Category: Zhang, W.]]		[[Category: Zhang, W.]]
-	[[Category: LLL]]
-	[[Category: MG]]
	[[Category: ribosome]]		[[Category: ribosome]]
	[[Category: rna-protein complex]]		[[Category: rna-protein complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 18~~:23:53 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:47:09 2008''