5jx4 - Revision history

OCA at 19:13, 20 September 2023

OCA — Wed, 20 Sep 2023 19:13:23 GMT

←Older revision		Revision as of 19:13, 20 September 2023
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	<StructureSection load='5jx4' size='340' side='right'caption='[[5jx4]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5jx4' size='340' side='right'caption='[[5jx4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jx4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JX4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JX4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jx4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JX4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</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=5jx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jx4 OCA], [~~http~~://pdbe.org/5jx4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jx4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jx4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jx4 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5jx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jx4 OCA], [https://pdbe.org/5jx4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jx4 RCSB], [https://www.ebi.ac.uk/pdbsum/5jx4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jx4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CSPB_BACCL CSPB_BACCL]] Affects cell viability at low temperatures.	+	[https://www.uniprot.org/uniprot/CSPB_BACCL CSPB_BACCL] Affects cell viability at low temperatures.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Babul, J]]	+	[[Category: Babul J]]
-	[[Category: Cabrejos, D]]	+	[[Category: Cabrejos D]]
-	[[Category: Cabrera, R]]	+	[[Category: Cabrera R]]
-	[[Category: Carvajal, A]]	+	[[Category: Carvajal A]]
-	[[Category: Castro-Fernandez, V]]	+	[[Category: Castro-Fernandez V]]
-	[[Category: Fuentealba, M]]	+	[[Category: Fuentealba M]]
-	[[Category: Garratt~~, R C~~]]	+	[[Category: Garratt RC]]
-	[[Category: Komives~~, E A~~]]	+	[[Category: Komives EA]]
-	[[Category: Pereira~~, H M~~]]	+	[[Category: Pereira HM]]
-	[[Category: Ramirez-Sarmiento~~, C A~~]]	+	[[Category: Ramirez-Sarmiento CA]]
-	[[Category: Vallejos, G]]	+	[[Category: Vallejos G]]
-	~~[[Category: Bccsp]]~~	+
-	~~[[Category: Cold shock protein]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Monomer]]~~	+
-	~~[[Category: Mutant~~]]	+

OCA at 11:43, 17 June 2020

OCA — Wed, 17 Jun 2020 11:43:42 GMT

←Older revision		Revision as of 11:43, 17 June 2020
Line 1:		Line 1:

	==Crystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein.==		==Crystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein.==
-	<StructureSection load='5jx4' size='340' side='right' caption='[[5jx4]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5jx4' size='340' side='right'caption='[[5jx4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jx4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JX4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JX4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jx4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JX4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JX4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5jx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jx4 OCA], [http://pdbe.org/5jx4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jx4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jx4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jx4 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=5jx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jx4 OCA], [http://pdbe.org/5jx4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jx4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jx4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jx4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Babul, J]]		[[Category: Babul, J]]
	[[Category: Cabrejos, D]]		[[Category: Cabrejos, D]]

OCA at 12:52, 10 May 2017

OCA — Wed, 10 May 2017 12:52:38 GMT

←Older revision		Revision as of 12:52, 10 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jx4 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein.==
		+	<StructureSection load='5jx4' size='340' side='right' caption='[[5jx4]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jx4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JX4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5jx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jx4 OCA], [http://pdbe.org/5jx4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jx4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jx4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jx4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CSPB_BACCL CSPB_BACCL]] Affects cell viability at low temperatures.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cold shock proteins (Csp) constitute a family of ubiquitous small proteins that act as RNA-chaperones to avoid cold-induced termination of translation. All members contain two subdomains composed of 2 and 3 beta-strands respectively, which are connected by a hinge loop and fold into a beta-barrel. Bacillus caldolyticus Csp (BcCsp) is one of the most studied members of the family in terms of its folding, function and structure. This protein has been described as a monomer in solution, although a recent crystal structure showed dimerization via domain swapping (DS). In contrast, other cold shock proteins of the same fold are known to dimerize in a non-swapped arrangement. Hypothesizing that reducing the size of the hinge loop may promote swapping as in several other DS proteins with different folds we deleted two residues from these region (BcCsp36-37), leading to a protein in monomer-dimer equilibrium with similar folding stability to that of the wild-type. Strikingly, the crystal structure of BcCsp36-37 revealed a non-swapped dimer with its interface located at the nucleic acid-binding surface, showing that the deletion led to structural consequences far from the perturbation site. Concomitantly, circular dichroism experiments on BcCsp36-37 demonstrated that binding of the oligonucleotide hexathymidine disrupts the dimer. Additionally, HDXMS shows a protective effect on the protein structure upon dimerization, where the resulting interactions between ligand-binding surfaces in the dimer reduced the extent of exchange throughout the whole protein. Our work provides evidence of the complex interplay between conformational dynamics, deletions and oligomerization within the Csp protein family. This article is protected by copyright. All rights reserved.

-	~~Authors:~~ Carvajal, A., Castro-Fernandez, V., ~~Cabrejos, D., Fuentealba, M., Pereira, H.M., Vallejos, G., Cabrera, R.~~, Garratt~~, R.C., Komives, E.A.~~, Ramirez-Sarmiento~~, C.A.~~, Babul, J.	+	Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics.,Carvajal AI, Vallejos G, Komives EA, Castro-Fernandez V, Leonardo DA, Garratt RC, Ramirez-Sarmiento CA, Babul J FEBS J. 2017 Apr 29. doi: 10.1111/febs.14093. PMID:28457014<ref>PMID:28457014</ref>

-	~~Description: Crystal structure of E36-G37del mutant~~ of the ~~Bacillus caldolyticus cold shock protein~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Fuentealba, M]]~~	+	<div class="pdbe-citations 5jx4" style="background-color:#fffaf0;"></div>
-	~~[[Category: Ramirez~~-~~Sarmiento, C.A]]~~	+	== References ==
-	~~[[Category: Castro~~-~~Fernandez, V]]~~	+	<references/>
-	~~[[Category~~: ~~Vallejos, G]]~~	+	__TOC__
-	~~[[Category: Cabrejos, D]]~~	+	</StructureSection>
-	~~[[Category: Garratt, R.C]]~~	+
-	~~[[Category: Pereira, H.M]]~~	+
	[[Category: Babul, J]]		[[Category: Babul, J]]
		+	[[Category: Cabrejos, D]]
	[[Category: Cabrera, R]]		[[Category: Cabrera, R]]
-	[[Category: Komives, E.A]]
	[[Category: Carvajal, A]]		[[Category: Carvajal, A]]
		+	[[Category: Castro-Fernandez, V]]
		+	[[Category: Fuentealba, M]]
		+	[[Category: Garratt, R C]]
		+	[[Category: Komives, E A]]
		+	[[Category: Pereira, H M]]
		+	[[Category: Ramirez-Sarmiento, C A]]
		+	[[Category: Vallejos, G]]
		+	[[Category: Bccsp]]
		+	[[Category: Cold shock protein]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Monomer]]
		+	[[Category: Mutant]]

OCA at 10:04, 9 March 2017

OCA — Thu, 09 Mar 2017 10:04:41 GMT

←Older revision		Revision as of 10:04, 9 March 2017
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Fuentealba, M]]		[[Category: Fuentealba, M]]
		+	[[Category: Ramirez-Sarmiento, C.A]]
	[[Category: Castro-Fernandez, V]]		[[Category: Castro-Fernandez, V]]
	[[Category: Vallejos, G]]		[[Category: Vallejos, G]]
		+	[[Category: Cabrejos, D]]
	[[Category: Garratt, R.C]]		[[Category: Garratt, R.C]]
	[[Category: Pereira, H.M]]		[[Category: Pereira, H.M]]
-	[[Category: Carvajal, A]]
-	[[Category: Ramirez-Sarmiento, C.A]]
-	[[Category: Cabrejos, D]]
	[[Category: Babul, J]]		[[Category: Babul, J]]
	[[Category: Cabrera, R]]		[[Category: Cabrera, R]]
	[[Category: Komives, E.A]]		[[Category: Komives, E.A]]
		+	[[Category: Carvajal, A]]

OCA at 13:12, 20 June 2016

OCA — Mon, 20 Jun 2016 13:12:56 GMT

←Older revision		Revision as of 13:12, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jx4 is ON HOLD	+	The entry 5jx4 is ON HOLD until Paper Publication

	Authors: Carvajal, A., Castro-Fernandez, V., Cabrejos, D., Fuentealba, M., Pereira, H.M., Vallejos, G., Cabrera, R., Garratt, R.C., Komives, E.A., Ramirez-Sarmiento, C.A., Babul, J.		Authors: Carvajal, A., Castro-Fernandez, V., Cabrejos, D., Fuentealba, M., Pereira, H.M., Vallejos, G., Cabrera, R., Garratt, R.C., Komives, E.A., Ramirez-Sarmiento, C.A., Babul, J.

OCA: Protected "5jx4" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 13:58:49 GMT

Protected "5jx4" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:58, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jx4 is ON HOLD Authors: Carvajal, A., Castro-Fernandez, V., Cabrejos, D., Fuentealba, M., Pereira, H.M., Vallejos, G., Cabrera, R., Garratt, R.C., ...

OCA — Wed, 01 Jun 2016 13:58:48 GMT

New page: '''Unreleased structure''' The entry 5jx4 is ON HOLD Authors: Carvajal, A., Castro-Fernandez, V., Cabrejos, D., Fuentealba, M., Pereira, H.M., Vallejos, G., Cabrera, R., Garratt, R.C., ...

New page

'''Unreleased structure'''

The entry 5jx4 is ON HOLD

Authors: Carvajal, A., Castro-Fernandez, V., Cabrejos, D., Fuentealba, M., Pereira, H.M., Vallejos, G., Cabrera, R., Garratt, R.C., Komives, E.A., Ramirez-Sarmiento, C.A., Babul, J.

Description: Crystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein.
[[Category: Unreleased Structures]]
[[Category: Fuentealba, M]]
[[Category: Castro-Fernandez, V]]
[[Category: Vallejos, G]]
[[Category: Garratt, R.C]]
[[Category: Pereira, H.M]]
[[Category: Carvajal, A]]
[[Category: Ramirez-Sarmiento, C.A]]
[[Category: Cabrejos, D]]
[[Category: Babul, J]]
[[Category: Cabrera, R]]
[[Category: Komives, E.A]]