3v7e - Revision history

OCA at 14:20, 14 March 2024

2024-03-14T14:20:10Z

←Older revision		Revision as of 14:20, 14 March 2024
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	<StructureSection load='3v7e' size='340' side='right'caption='[[3v7e]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3v7e' size='340' side='right'caption='[[3v7e]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V7E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V7E FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3v7q\|3v7q]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])~~</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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [https://pdbe.org/3v7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [https://www.ebi.ac.uk/pdbsum/3v7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7e ProSAT]</span></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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [https://pdbe.org/3v7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [https://www.ebi.ac.uk/pdbsum/3v7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7e ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/RXL7_BACSU RXL7_BACSU]
-	The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) approximately 270 nM and approximately 2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. ~~The biological functions of YbxF and YlxQ remain to be determined~~.	+

-	~~YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.,Baird NJ, Zhang J, Hamma T, Ferre-D'Amare AR RNA. 2012 Feb 21. PMID:22355167<ref>PMID:22355167</ref>~~	+	==See Also==
-		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3v7e" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
		+	[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Amare, A R.Ferre-D~~]]	+	[[Category: Baird NJ]]
-	[[Category: ~~Baird, N J~~]]	+	[[Category: Ferre-D'Amare AR]]
-	[[Category: Hamma, T]]	+	[[Category: Hamma T]]
-	[[Category: Zhang, J]]	+	[[Category: Zhang J]]
-	~~[[Category: A member of the l7ae/l30e superfamily]]~~	+
-	~~[[Category: K-turn]]~~	+
-	~~[[Category: K-turn motif]]~~	+
-	~~[[Category: L7ae-like]]~~	+
-	~~[[Category: Ribosomal protein-rna complex]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna-protein complex]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 08:37, 20 July 2022

2022-07-20T08:37:37Z

←Older revision		Revision as of 08:37, 20 July 2022
Line 1:		Line 1:

	==Crystal structure of YbxF bound to the SAM-I riboswitch aptamer==		==Crystal structure of YbxF bound to the SAM-I riboswitch aptamer==
-	<StructureSection load='3v7e' size='340' side='right' caption='[[3v7e]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='3v7e' size='340' side='right'caption='[[3v7e]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3V7E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V7E 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>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3v7q\|3v7q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3v7q\|3v7q]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [~~http~~://pdbe.org/3v7e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3v7e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7e ProSAT]</span></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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [https://pdbe.org/3v7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [https://www.ebi.ac.uk/pdbsum/3v7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Amare, A R.Ferre-D]]		[[Category: Amare, A R.Ferre-D]]
	[[Category: Baird, N J]]		[[Category: Baird, N J]]

OCA at 19:09, 11 August 2016

2016-08-11T19:09:34Z

←Older revision		Revision as of 19:09, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of YbxF bound to the SAM-I riboswitch aptamer==		==Crystal structure of YbxF bound to the SAM-I riboswitch aptamer==
	<StructureSection load='3v7e' size='340' side='right' caption='[[3v7e]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3v7e' size='340' side='right' caption='[[3v7e]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V7E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V7E 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>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3v7q\|3v7q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3v7q\|3v7q]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [http://www.ebi.ac.uk/pdbsum/3v7e 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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [http://pdbe.org/3v7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [http://www.ebi.ac.uk/pdbsum/3v7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3v7e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Amare, A R.Ferre-D]]		[[Category: Amare, A R.Ferre-D]]
	[[Category: Baird, N J]]		[[Category: Baird, N J]]

OCA at 10:46, 4 January 2015

2015-01-04T10:46:10Z

←Older revision		Revision as of 10:46, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V7E FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene><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>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3v7q\|3v7q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3v7q\|3v7q]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [http://www.ebi.ac.uk/pdbsum/3v7e 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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [http://www.ebi.ac.uk/pdbsum/3v7e PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.,Baird NJ, Zhang J, Hamma T, Ferre-D'Amare AR RNA. 2012 Feb 21. PMID:22355167<ref>PMID:22355167</ref>		YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.,Baird NJ, Zhang J, Hamma T, Ferre-D'Amare AR RNA. 2012 Feb 21. PMID:22355167<ref>PMID:22355167</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Amare, A R.Ferre-D.]]	+	[[Category: Amare, A R.Ferre-D]]
-	[[Category: Baird, N J.]]	+	[[Category: Baird, N J]]
-	[[Category: Hamma, T.]]	+	[[Category: Hamma, T]]
-	[[Category: Zhang, J.]]	+	[[Category: Zhang, J]]
	[[Category: A member of the l7ae/l30e superfamily]]		[[Category: A member of the l7ae/l30e superfamily]]
	[[Category: K-turn]]		[[Category: K-turn]]

OCA at 06:21, 5 June 2014

2014-06-05T06:21:24Z

←Older revision		Revision as of 06:21, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3v7e.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of YbxF bound to the SAM-I riboswitch aptamer==
		+	<StructureSection load='3v7e' size='340' side='right' caption='[[3v7e]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V7E FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3v7q\|3v7q]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [http://www.ebi.ac.uk/pdbsum/3v7e PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) approximately 270 nM and approximately 2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.

-	<!--	+	YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.,Baird NJ, Zhang J, Hamma T, Ferre-D'Amare AR RNA. 2012 Feb 21. PMID:22355167<ref>PMID:22355167</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3v7e"~~, ~~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_3v7e\| PDB=3v7e \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~YbxF bound to~~ the ~~SAM-I riboswitch aptamer===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22355167}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22355167 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22355167}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3v7e]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022355167<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Amare, A R.Ferre-D.]]		[[Category: Amare, A R.Ferre-D.]]

OCA at 06:54, 18 April 2012

2012-04-18T06:54:36Z

←Older revision		Revision as of 06:54, 18 April 2012
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-	[[Image:3v7e.~~jpg~~\|left\|200px]]	+	[[Image:3v7e.png\|left\|200px]]

	<!--		<!--

OCA at 05:45, 8 March 2012

2012-03-08T05:45:22Z

←Older revision		Revision as of 05:45, 8 March 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:3v7e.jpg\|left\|200px]]

-	The ~~entry 3v7e~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3v7e", 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_3v7e\| PDB=3v7e \| SCENE= }}

-	~~Authors: Baird, N.J., Zhang, J., Hamma, T., Ferre~~-~~D'Amare, A.R.~~	+	===Crystal structure of YbxF bound to the SAM-I riboswitch aptamer===

-	~~Description~~: ~~Crystal~~ structure of ~~YbxF bound to~~ the ~~SAM~~-~~I riboswitch aptamer~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22355167}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22355167 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22355167}}
		+
		+	==About this Structure==
		+	[[3v7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022355167</ref><references group="xtra"/>
		+	[[Category: Bacillus subtilis]]
		+	[[Category: Amare, A R.Ferre-D.]]
		+	[[Category: Baird, N J.]]
		+	[[Category: Hamma, T.]]
		+	[[Category: Zhang, J.]]
		+	[[Category: A member of the l7ae/l30e superfamily]]
		+	[[Category: K-turn]]
		+	[[Category: K-turn motif]]
		+	[[Category: L7ae-like]]
		+	[[Category: Ribosomal protein-rna complex]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna-protein complex]]
		+	[[Category: Unknown function]]

OCA: Protected "3v7e" [edit=sysop:move=sysop]

2011-12-28T06:53:35Z

Protected "3v7e" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:53, 28 December 2011

OCA: New page: '''Unreleased structure''' The entry 3v7e is ON HOLD Authors: Baird, N.J., Zhang, J., Hamma, T., Ferre-D'Amare, A.R. Description: Crystal structure of YbxF bound to the SAM-I riboswitc...

2011-12-28T06:53:34Z

New page: '''Unreleased structure''' The entry 3v7e is ON HOLD Authors: Baird, N.J., Zhang, J., Hamma, T., Ferre-D'Amare, A.R. Description: Crystal structure of YbxF bound to the SAM-I riboswitc...

New page

'''Unreleased structure'''

The entry 3v7e is ON HOLD

Authors: Baird, N.J., Zhang, J., Hamma, T., Ferre-D'Amare, A.R.

Description: Crystal structure of YbxF bound to the SAM-I riboswitch aptamer