5eev - Revision history

OCA at 06:23, 5 July 2023

2023-07-05T06:23:34Z

←Older revision		Revision as of 06:23, 5 July 2023
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	<StructureSection load='5eev' size='340' side='right'caption='[[5eev]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='5eev' size='340' side='right'caption='[[5eev]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5eev]] is a 23 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EEV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5eev]] is a 23 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EEV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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]] 1.98Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[1gtf\|1gtf]], [[5eeu\|5eeu]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></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=5eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eev OCA], [~~http~~://pdbe.org/5eev PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5eev RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5eev PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5eev 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=5eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eev OCA], [https://pdbe.org/5eev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eev RCSB], [https://www.ebi.ac.uk/pdbsum/5eev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eev ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MTRB_GEOSE MTRB_GEOSE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bury, C S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Garman, E F~~]]	+	[[Category: Bury CS]]
-	[[Category: ~~McGeehan, J E~~]]	+	[[Category: Garman EF]]
-	[[Category: ~~Shevtsov, M B~~]]	+	[[Category: McGeehan JE]]
-	[[Category: ~~Protein-rna complex]]~~	+	[[Category: Shevtsov MB]]
-	~~[[Category: Radiation damage]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna-binding protein~~]]	+

OCA at 06:55, 22 April 2020

2020-04-22T06:55:44Z

←Older revision		Revision as of 06:55, 22 April 2020
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	==RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 3.88 MGy==		==RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 3.88 MGy==
-	<StructureSection load='5eev' size='340' side='right' caption='[[5eev]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='5eev' size='340' side='right'caption='[[5eev]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5eev]] is a 23 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EEV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5eev]] is a 23 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EEV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gtf\|1gtf]], [[5eeu\|5eeu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gtf\|1gtf]], [[5eeu\|5eeu]]</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=5eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eev OCA], [http://pdbe.org/5eev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eev RCSB], [http://www.ebi.ac.uk/pdbsum/5eev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eev 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=5eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eev OCA], [http://pdbe.org/5eev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eev RCSB], [http://www.ebi.ac.uk/pdbsum/5eev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eev 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: Bury, C S]]		[[Category: Bury, C S]]
	[[Category: Garman, E F]]		[[Category: Garman, E F]]

OCA at 10:53, 13 September 2017

2017-09-13T10:53:56Z

←Older revision		Revision as of 10:53, 13 September 2017
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gtf\|1gtf]], [[5eeu\|5eeu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gtf\|1gtf]], [[5eeu\|5eeu]]</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=5eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eev OCA], [http://pdbe.org/5eev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eev RCSB], [http://www.ebi.ac.uk/pdbsum/5eev 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=5eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eev OCA], [http://pdbe.org/5eev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eev RCSB], [http://www.ebi.ac.uk/pdbsum/5eev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eev ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Protein-rna complex]]		[[Category: Protein-rna complex]]
	[[Category: Radiation damage]]		[[Category: Radiation damage]]
		+	[[Category: Rna binding protein]]
	[[Category: Rna-binding protein]]		[[Category: Rna-binding protein]]

OCA at 03:40, 11 May 2016

2016-05-11T03:40:07Z

←Older revision		Revision as of 03:40, 11 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5eev is ~~ON HOLD until Paper~~ Publication	+	==RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 3.88 MGy==
		+	<StructureSection load='5eev' size='340' side='right' caption='[[5eev]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5eev]] is a 23 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EEV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gtf\|1gtf]], [[5eeu\|5eeu]]</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=5eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eev OCA], [http://pdbe.org/5eev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eev RCSB], [http://www.ebi.ac.uk/pdbsum/5eev PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 A) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.

-	~~Authors: Bury, C.S~~., McGeehan, ~~J.E.~~, ~~Garman~~, ~~E.F.~~, Shevtsov, M.B.	+	RNA protects a nucleoprotein complex against radiation damage.,Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF Acta Crystallogr D Struct Biol. 2016 May 1;72(Pt 5):648-57. doi:, 10.1107/S2059798316003351. Epub 2016 Apr 26. PMID:27139628<ref>PMID:27139628</ref>

-	~~Description: RADIATION DAMAGE TO THE TRAP~~-~~RNA COMPLEX~~: ~~DOSE (DWD) 3.88 MGy~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Garman, E.F]]	+	<div class="pdbe-citations 5eev" style="background-color:#fffaf0;"></div>
-	[[Category: Shevtsov, M.B]]	+	== References ==
-	[[Category: ~~Bury, C.S~~]]	+	<references/>
-	[[Category: ~~Mcgeehan, J.E~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bury, C S]]
		+	[[Category: Garman, E F]]
		+	[[Category: McGeehan, J E]]
		+	[[Category: Shevtsov, M B]]
		+	[[Category: Protein-rna complex]]
		+	[[Category: Radiation damage]]
		+	[[Category: Rna-binding protein]]

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

2015-12-01T02:44:45Z

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

←Older revision

Revision as of 02:44, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5eev is ON HOLD until Paper Publication Authors: Bury, C.S., McGeehan, J.E., Garman, E.F., Shevtsov, M.B. Description: RADIATION DAMAGE TO THE TRAP...

2015-12-01T02:44:44Z

New page: '''Unreleased structure''' The entry 5eev is ON HOLD until Paper Publication Authors: Bury, C.S., McGeehan, J.E., Garman, E.F., Shevtsov, M.B. Description: RADIATION DAMAGE TO THE TRAP...

New page

'''Unreleased structure'''

The entry 5eev is ON HOLD until Paper Publication

Authors: Bury, C.S., McGeehan, J.E., Garman, E.F., Shevtsov, M.B.

Description: RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 3.88 MGy
[[Category: Unreleased Structures]]
[[Category: Garman, E.F]]
[[Category: Shevtsov, M.B]]
[[Category: Bury, C.S]]
[[Category: Mcgeehan, J.E]]