6ado - Revision history

OCA at 10:31, 27 March 2024

2024-03-27T10:31:31Z

←Older revision		Revision as of 10:31, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6ado' size='340' side='right'caption='[[6ado]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6ado' size='340' side='right'caption='[[6ado]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ado]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Leido Leido~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ADO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ADO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ado]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_donovani Leishmania donovani]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ADO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ADO FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~5cx2~~\|~~5cx2~~]]</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]] 2.502Å</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=6ado FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ado OCA], [~~http~~://pdbe.org/6ado PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ado RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ado PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ado 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=6ado FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ado OCA], [https://pdbe.org/6ado PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ado RCSB], [https://www.ebi.ac.uk/pdbsum/6ado PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ado ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q3T1U8_LEIDO Q3T1U8_LEIDO]
-	Protein-protein interactions of cellular importance are mediated by coiled coils (CCs), the ubiquitous structural motif formed by the association of two or more alpha-helices in a knobs into holes manner. Coronins, actin-associated multi-functional proteins that possess distinct cytoskeleton-dependent and independent functions, oligomerize through their C-terminal CC domain. The structure of the L. donovani coronin CC domain (LdCoroCC; PDB ID 5CX2) revealed, in addition to a novel topology and architecture, an inherent asymmetry, with one of the helices of the 4-helix bundle axially shifted ( approximately 2 turns). The structural analysis identified that steric hindrance by Ile 486, Leu 493 and Met 500 as the cause for this asymmetry. To experimentally validate this hypothesis and to better understand the sequence-structure relationship in CCs, these amino acids have been mutated (I486A, L493A, M500V and the double mutant I486A-L493A) and characterized. Thermal CD studies suggest that the I486A and M500V mutants have comparable Tm values to LdCoroCC, while the other mutants have lower melting temperatures. The mutant crystal structures (I486A, M500V and the double mutant) retain the 'ade' core packing as LdcoroCC. While the M500V structure is similar to LdCoroCC, the I486A and the I486A-L493A structures show an asymmetry to symmetry transition. This study reveals crucial role of residues at position 'a' in coiled-coil domain play an important role in stabilizing the asymmetry in LdCoroCC, which might be necessary pursue specific biological function(s) inside the Leishmania.	+
-		+
-	Molecular and Structural analysis of a mechanical transition of helices in the L. donovani coronin coiled-coil domain.,Shrimant Karade S, Ansari A, Kumar Srivastava V, Ranjan Nayak A, Venkatesh Pratap J Int J Biol Macromol. 2019 Nov 25. pii: ~~S0141-8130(19)31056-6. doi:, 10.1016~~/~~j.ijbiomac.2019.09.138. PMID:31778699<ref>PMID:31778699<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6ado" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leido~~]]	+	[[Category: Leishmania donovani]]
-	[[Category: Ansari, A]]	+	[[Category: Ansari A]]
-	[[Category: Karade~~, S S~~]]	+	[[Category: Karade SS]]
-	[[Category: Pratap~~, J V]]~~	+	[[Category: Pratap JV]]
-	~~[[Category: Mutant of actin-associated protein coronin of leishmania donovani]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 17:37, 11 December 2019

2019-12-11T17:37:37Z

←Older revision		Revision as of 17:37, 11 December 2019
Line 3:		Line 3:
	<StructureSection load='6ado' size='340' side='right'caption='[[6ado]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6ado' size='340' side='right'caption='[[6ado]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ado]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ADO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ADO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ado]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Leido Leido]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ADO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ADO FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cx2\|5cx2]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cx2\|5cx2]]</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=6ado FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ado OCA], [http://pdbe.org/6ado PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ado RCSB], [http://www.ebi.ac.uk/pdbsum/6ado PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ado 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=6ado FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ado OCA], [http://pdbe.org/6ado PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ado RCSB], [http://www.ebi.ac.uk/pdbsum/6ado PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ado ProSAT]</span></td></tr>
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Coiled coils are ubiquitous structural motifs that serve as a platform for protein~~-protein interactions ~~and play a central role in myriad physiological processes. Though the formation~~ of a coiled ~~coil requires only~~ the ~~presence~~ of ~~suitably spaced hydrophobic residues, sequence specificities have also been associated with specific oligomeric states. RhXXhE is one such sequence motif, associated with parallel trimers, found~~ in ~~coronins and other proteins~~. ~~Coronin~~, ~~present in all eukaryotes, is an~~ actin-associated ~~protein involved in regulating actin turnover. Most eukaryotic coronins~~ possess ~~the RhXXhE trimerization motif. However~~, ~~a unique feature of parasitic kinetoplastid coronin is that the positions of R and E are swapped within~~ their ~~coiled coil~~ domain~~, but were still expected to form trimers~~. ~~To understand the role~~ of ~~swapped motif in oligomeric specificity, we determined~~ the ~~X-ray crystal structure of Leishmania~~ donovani coronin ~~coiled coil~~ domain (LdCoroCC) ~~at 2.2A~~, ~~which surprisingly, reveals an anti-parallel tetramer assembly. Small angle X-ray scattering studies and chemical crosslinking confirm the tetramer~~ in ~~solution~~ and ~~is consistent with the oligomerization observed in the full length protein. Structural analyses reveal that LdCoroCC possesses~~ an inherent asymmetry, ~~in that~~ one of the helices of the bundle is axially shifted ~~with respect to the other three~~. The analysis ~~also identifies steric reasons~~ that cause this asymmetry. ~~The bundle adapts an extended a~~-d-~~e core packing~~, the ~~e residue being polar~~ (~~with an exception~~) ~~which results in a thermostable bundle with polar and apolar interfaces~~, ~~unlike~~ the ~~existing a~~-~~d-e core antiparallel homotetramers with apolar core~~. ~~Functional implications~~ of ~~the anti~~-~~parallel association~~ in ~~kinetoplastids are discussed~~.	+	Protein-protein interactions of cellular importance are mediated by coiled coils (CCs), the ubiquitous structural motif formed by the association of two or more alpha-helices in a knobs into holes manner. Coronins, actin-associated multi-functional proteins that possess distinct cytoskeleton-dependent and independent functions, oligomerize through their C-terminal CC domain. The structure of the L. donovani coronin CC domain (LdCoroCC; PDB ID 5CX2) revealed, in addition to a novel topology and architecture, an inherent asymmetry, with one of the helices of the 4-helix bundle axially shifted ( approximately 2 turns). The structural analysis identified that steric hindrance by Ile 486, Leu 493 and Met 500 as the cause for this asymmetry. To experimentally validate this hypothesis and to better understand the sequence-structure relationship in CCs, these amino acids have been mutated (I486A, L493A, M500V and the double mutant I486A-L493A) and characterized. Thermal CD studies suggest that the I486A and M500V mutants have comparable Tm values to LdCoroCC, while the other mutants have lower melting temperatures. The mutant crystal structures (I486A, M500V and the double mutant) retain the 'ade' core packing as LdcoroCC. While the M500V structure is similar to LdCoroCC, the I486A and the I486A-L493A structures show an asymmetry to symmetry transition. This study reveals crucial role of residues at position 'a' in coiled-coil domain play an important role in stabilizing the asymmetry in LdCoroCC, which might be necessary pursue specific biological function(s) inside the Leishmania.

-	~~Structure~~ of ~~Leishmania~~ donovani coronin coiled coil domain ~~reveals an antiparallel 4 helix bundle with inherent asymmetry~~.,~~Nayak AR,~~ Karade SS, Srivastava VK, ~~Rana AK, Gupta CM, Sahasrabuddhe AA~~, Pratap JV J ~~Struct~~ Biol. ~~2016 Jul;195~~(1)~~:129~~-38. doi: 10.1016/j.~~jsb~~.~~2016~~.02.~~020. Epub 2016 , Mar 2~~. PMID:~~26940672~~<ref>PMID:~~26940672~~</ref>	+	Molecular and Structural analysis of a mechanical transition of helices in the L. donovani coronin coiled-coil domain.,Shrimant Karade S, Ansari A, Kumar Srivastava V, Ranjan Nayak A, Venkatesh Pratap J Int J Biol Macromol. 2019 Nov 25. pii: S0141-8130(19)31056-6. doi:, 10.1016/j.ijbiomac.2019.09.138. PMID:31778699<ref>PMID:31778699</ref>

	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>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Leido]]
	[[Category: Ansari, A]]		[[Category: Ansari, A]]
	[[Category: Karade, S S]]		[[Category: Karade, S S]]

OCA at 05:12, 10 October 2019

2019-10-10T05:12:07Z

←Older revision		Revision as of 05:12, 10 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ado is ~~ON HOLD until Paper~~ Publication	+	==LdCoroCC mutant-I486A==
		+	<StructureSection load='6ado' size='340' side='right'caption='[[6ado]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ado]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ADO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ADO FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cx2\|5cx2]]</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=6ado FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ado OCA], [http://pdbe.org/6ado PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ado RCSB], [http://www.ebi.ac.uk/pdbsum/6ado PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ado ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Coiled coils are ubiquitous structural motifs that serve as a platform for protein-protein interactions and play a central role in myriad physiological processes. Though the formation of a coiled coil requires only the presence of suitably spaced hydrophobic residues, sequence specificities have also been associated with specific oligomeric states. RhXXhE is one such sequence motif, associated with parallel trimers, found in coronins and other proteins. Coronin, present in all eukaryotes, is an actin-associated protein involved in regulating actin turnover. Most eukaryotic coronins possess the RhXXhE trimerization motif. However, a unique feature of parasitic kinetoplastid coronin is that the positions of R and E are swapped within their coiled coil domain, but were still expected to form trimers. To understand the role of swapped motif in oligomeric specificity, we determined the X-ray crystal structure of Leishmania donovani coronin coiled coil domain (LdCoroCC) at 2.2A, which surprisingly, reveals an anti-parallel tetramer assembly. Small angle X-ray scattering studies and chemical crosslinking confirm the tetramer in solution and is consistent with the oligomerization observed in the full length protein. Structural analyses reveal that LdCoroCC possesses an inherent asymmetry, in that one of the helices of the bundle is axially shifted with respect to the other three. The analysis also identifies steric reasons that cause this asymmetry. The bundle adapts an extended a-d-e core packing, the e residue being polar (with an exception) which results in a thermostable bundle with polar and apolar interfaces, unlike the existing a-d-e core antiparallel homotetramers with apolar core. Functional implications of the anti-parallel association in kinetoplastids are discussed.

-	~~Authors:~~ Karade, ~~S.S.~~, ~~Ansari~~, A., ~~Pratap~~, J.V.	+	Structure of Leishmania donovani coronin coiled coil domain reveals an antiparallel 4 helix bundle with inherent asymmetry.,Nayak AR, Karade SS, Srivastava VK, Rana AK, Gupta CM, Sahasrabuddhe AA, Pratap JV J Struct Biol. 2016 Jul;195(1):129-38. doi: 10.1016/j.jsb.2016.02.020. Epub 2016 , Mar 2. PMID:26940672<ref>PMID:26940672</ref>

-	~~Description: LdCoroCC mutant-I486A~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Pratap, J.V]]~~	+	<div class="pdbe-citations 6ado" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Karade, S.S~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ansari, A]]		[[Category: Ansari, A]]
		+	[[Category: Karade, S S]]
		+	[[Category: Pratap, J V]]
		+	[[Category: Mutant of actin-associated protein coronin of leishmania donovani]]
		+	[[Category: Structural protein]]

OCA at 05:53, 12 September 2018

2018-09-12T05:53:33Z

←Older revision		Revision as of 05:53, 12 September 2018
Line 3:		Line 3:
	The entry 6ado is ON HOLD until Paper Publication		The entry 6ado is ON HOLD until Paper Publication

-	Authors: ~~Pratap, J.V.,~~ Karade, S.S., Ansari, A.	+	Authors: Karade, S.S., Ansari, A., Pratap, J.V.

	Description: LdCoroCC mutant-I486A		Description: LdCoroCC mutant-I486A

OCA at 14:37, 15 August 2018

2018-08-15T14:37:15Z

←Older revision		Revision as of 14:37, 15 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ado is ON HOLD	+	The entry 6ado is ON HOLD until Paper Publication

-	Authors: Pratap, J.V., ~~Shrimant~~, K.S., Ansari, A.	+	Authors: Pratap, J.V., Karade, S.S., Ansari, A.

	Description: LdCoroCC mutant-I486A		Description: LdCoroCC mutant-I486A
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Pratap, J.V]]		[[Category: Pratap, J.V]]
-	[[Category: ~~Shrimant~~, K.S]]	+	[[Category: Karade, S.S]]
	[[Category: Ansari, A]]		[[Category: Ansari, A]]

OCA: Protected "6ado" [edit=sysop:move=sysop]

2018-08-09T19:43:38Z

Protected "6ado" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:43, 9 August 2018

OCA: New page: '''Unreleased structure''' The entry 6ado is ON HOLD Authors: Pratap, J.V., Shrimant, K.S., Ansari, A. Description: LdCoroCC mutant-I486A Category: Unreleased Structures [[Category...

2018-08-09T19:43:37Z

New page: '''Unreleased structure''' The entry 6ado is ON HOLD Authors: Pratap, J.V., Shrimant, K.S., Ansari, A. Description: LdCoroCC mutant-I486A Category: Unreleased Structures [[Category...

New page

'''Unreleased structure'''

The entry 6ado is ON HOLD

Authors: Pratap, J.V., Shrimant, K.S., Ansari, A.

Description: LdCoroCC mutant-I486A
[[Category: Unreleased Structures]]
[[Category: Pratap, J.V]]
[[Category: Shrimant, K.S]]
[[Category: Ansari, A]]