4wfm - Revision history

OCA at 11:27, 9 May 2024

OCA — Thu, 09 May 2024 11:27:41 GMT

←Older revision		Revision as of 11:27, 9 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wfm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WFM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wfm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WFM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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]] 3.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=4wfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wfm OCA], [https://pdbe.org/4wfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wfm RCSB], [https://www.ebi.ac.uk/pdbsum/4wfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wfm 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=4wfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wfm OCA], [https://pdbe.org/4wfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wfm RCSB], [https://www.ebi.ac.uk/pdbsum/4wfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wfm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:06, 7 April 2023

OCA — Fri, 07 Apr 2023 07:06:43 GMT

←Older revision		Revision as of 07:06, 7 April 2023
Line 3:		Line 3:
	<StructureSection load='4wfm' size='340' side='right'caption='[[4wfm]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4wfm' size='340' side='right'caption='[[4wfm]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wfm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WFM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wfm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WFM 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>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~CCC~~:~~CYTIDINE-5-PHOSPHATE-2,3-CYCLIC~~+~~PHOSPHATE~~'>~~CCC~~</scene>, <scene name='pdbligand=~~GTP~~:~~GUANOSINE-5-TRIPHOSPHATE~~'>~~GTP~~</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=4wfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wfm OCA], [https://pdbe.org/4wfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wfm RCSB], [https://www.ebi.ac.uk/pdbsum/4wfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wfm ProSAT]</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=4wfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wfm OCA], [~~http~~://pdbe.org/4wfm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wfm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wfm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wfm ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kempf, G]]	+	[[Category: Kempf G]]
-	[[Category: Sinning, I]]	+	[[Category: Sinning I]]
-	[[Category: Wild, K]]	+	[[Category: Wild K]]
-	~~[[Category: Elongation arrest]]~~	+
-	~~[[Category: Non-coding]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Srp rna~~]]	+

OCA at 08:24, 23 May 2019

OCA — Thu, 23 May 2019 08:24:36 GMT

←Older revision		Revision as of 08:24, 23 May 2019
Line 1:		Line 1:

	==Structure of the complete bacterial SRP Alu domain==		==Structure of the complete bacterial SRP Alu domain==
-	<StructureSection load='4wfm' size='340' side='right' caption='[[4wfm]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='4wfm' size='340' side='right'caption='[[4wfm]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wfm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WFM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wfm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WFM FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kempf, G]]		[[Category: Kempf, G]]
	[[Category: Sinning, I]]		[[Category: Sinning, I]]

OCA at 16:10, 11 August 2016

OCA — Thu, 11 Aug 2016 16:10:50 GMT

←Older revision		Revision as of 16:10, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of the complete bacterial SRP Alu domain==		==Structure of the complete bacterial SRP Alu domain==
	<StructureSection load='4wfm' size='340' side='right' caption='[[4wfm]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4wfm' size='340' side='right' caption='[[4wfm]], [[Resolution\|resolution]] 3.10Å' scene=''>
Line 5:		Line 6:
	</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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></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=4wfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wfm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wfm RCSB], [http://www.ebi.ac.uk/pdbsum/4wfm 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=4wfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wfm OCA], [http://pdbe.org/4wfm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wfm RCSB], [http://www.ebi.ac.uk/pdbsum/4wfm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wfm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4wfm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:08, 19 November 2014

OCA — Wed, 19 Nov 2014 10:08:56 GMT

←Older revision		Revision as of 10:08, 19 November 2014
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Kempf, G.]]	+	[[Category: Kempf, G]]
-	[[Category: Sinning, I.]]	+	[[Category: Sinning, I]]
-	[[Category: Wild, K.]]	+	[[Category: Wild, K]]
	[[Category: Elongation arrest]]		[[Category: Elongation arrest]]
	[[Category: Non-coding]]		[[Category: Non-coding]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Srp rna]]		[[Category: Srp rna]]

OCA at 10:41, 20 October 2014

OCA — Mon, 20 Oct 2014 10:41:42 GMT

←Older revision		Revision as of 10:41, 20 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of the complete bacterial SRP Alu domain==
		+	<StructureSection load='4wfm' size='340' side='right' caption='[[4wfm]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4wfm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WFM 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></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></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=4wfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wfm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wfm RCSB], [http://www.ebi.ac.uk/pdbsum/4wfm PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Alu domain of the signal recognition particle (SRP) arrests protein biosynthesis by competition with elongation factor binding on the ribosome. The mammalian Alu domain is a protein-RNA complex, while prokaryotic Alu domains are protein-free with significant extensions of the RNA. Here we report the crystal structure of the complete Alu domain of Bacillus subtilis SRP RNA at 2.5 A resolution. The bacterial Alu RNA reveals a compact fold, which is stabilized by prokaryote-specific extensions and interactions. In this 'closed' conformation, the 5' and 3' regions are clamped together by the additional helix 1, the connecting 3-way junction and a novel minor groove interaction, which we term the 'minor-saddle motif' (MSM). The 5' region includes an extended loop-loop pseudoknot made of five consecutive Watson-Crick base pairs. Homology modeling with the human Alu domain in context of the ribosome shows that an additional lobe in the pseudoknot approaches the large subunit, while the absence of protein results in the detachment from the small subunit. Our findings provide the structural basis for purely RNA-driven elongation arrest in prokaryotes, and give insights into the structural adaption of SRP RNA during evolution.

-	~~The entry 4wfm is ON HOLD until Paper Publication~~	+	Structure of the complete bacterial SRP Alu domain.,Kempf G, Wild K, Sinning I Nucleic Acids Res. 2014 Sep 30. pii: gku883. PMID:25270875<ref>PMID:25270875</ref>

-	~~Authors~~: Kempf, G., Wild, K.~~, Sinning, I.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of the complete bacterial Alu domain~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kempf, G.]]
		+	[[Category: Sinning, I.]]
		+	[[Category: Wild, K.]]
		+	[[Category: Elongation arrest]]
		+	[[Category: Non-coding]]
		+	[[Category: Rna]]
		+	[[Category: Srp rna]]

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

OCA — Wed, 24 Sep 2014 09:14:10 GMT

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

←Older revision

Revision as of 09:14, 24 September 2014

OCA: New page: '''Unreleased structure''' The entry 4wfm is ON HOLD until Paper Publication Authors: Kempf, G., Wild, K., Sinning, I. Description: Structure of the complete bacterial Alu domain

OCA — Wed, 24 Sep 2014 09:14:08 GMT

New page: '''Unreleased structure''' The entry 4wfm is ON HOLD until Paper Publication Authors: Kempf, G., Wild, K., Sinning, I. Description: Structure of the complete bacterial Alu domain

New page

'''Unreleased structure'''

The entry 4wfm is ON HOLD until Paper Publication

Authors: Kempf, G., Wild, K., Sinning, I.

Description: Structure of the complete bacterial Alu domain