4dni - Revision history

OCA at 10:52, 1 March 2024

2024-03-01T10:52:29Z

←Older revision		Revision as of 10:52, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dni]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei] and [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei_TREU927 Trypanosoma brucei brucei TREU927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DNI FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dni]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei] and [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei_TREU927 Trypanosoma brucei brucei TREU927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DNI FirstGlance]. <br>
-	</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=4dni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dni OCA], [https://pdbe.org/4dni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dni RCSB], [https://www.ebi.ac.uk/pdbsum/4dni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dni ProSAT]</span></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]] 2.55Å</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=4dni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dni OCA], [https://pdbe.org/4dni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dni RCSB], [https://www.ebi.ac.uk/pdbsum/4dni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dni ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q38B90_TRYB2 Q38B90_TRYB2]] [[https://www.uniprot.org/uniprot/Q95W13_9TRYP Q95W13_9TRYP]]	+	[https://www.uniprot.org/uniprot/Q38B90_TRYB2 Q38B90_TRYB2] [https://www.uniprot.org/uniprot/Q95W13_9TRYP Q95W13_9TRYP]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Trypanosomatids form a group of protozoa which contain parasites of human, animals and plants. Several of these species cause major human diseases, including Trypanosoma brucei which is the causative agent of human African trypanosomiasis, also called sleeping sickness. These organisms have many highly unusual features including a unique U-insertion/deletion RNA editing process in the single mitochondrion. A key multi-protein complex, called the approximately 20S editosome, or editosome, carries out a cascade of essential RNA-modifying reactions and contains a core of 12 different proteins of which six are the interaction proteins A1 to A6. Each of these interaction proteins comprises a C-terminal OB-fold and the smallest interaction protein A6 has been shown to interact with four other editosome OB-folds. Here we report the results of a "linked OB-fold" approach to obtain a view of how multiple OB-folds might interact in the core of the editosome. Constructs with variants of linked domains in 25 expression and co-expression experiments resulted in 13 soluble multi-OB-fold complexes. In several instances, these complexes were more homogeneous in size than those obtained from corresponding unlinked OB-folds. The crystal structure of A3(OB) linked to A6 could be elucidated and confirmed the tight interaction between these two OB domains as seen also in our recent complex of A3(OB) and A6 with nanobodies. In the current crystal structure of A3(OB) linked to A6, hydrophobic side chains reside in well-defined pockets of neighboring OB-fold domains. When analyzing the available crystal structures of editosome OB-folds, it appears that in five instances "Pocket 1" of A1(OB), A3(OB) and A6 is occupied by a hydrophobic side chain from a neighboring protein. In these three different OB-folds, Pocket 1 is formed by two conserved sequence motifs and an invariant arginine. These pockets might play a key role in the assembly or mechanism of the editosome by interacting with hydrophobic side chains from other proteins.	+
-		+
-	Explorations of linked editosome domains leading to the discovery of motifs defining conserved pockets in editosome OB-folds.,Park YJ, Hol WG J Struct Biol. 2012 Nov;180(2):362-73. doi: 10.1016/j.jsb.2012.07.012. Epub 2012 , Aug 10. PMID:22902563<ref>PMID:22902563</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4dni" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:30, 21 September 2022

2022-09-21T08:30:34Z

←Older revision		Revision as of 08:30, 21 September 2022
Line 1:		Line 1:

	==Structure of Editosome protein==		==Structure of Editosome protein==
-	<StructureSection load='4dni' size='340' side='right' caption='[[4dni]], [[Resolution\|resolution]] 2.55Å' scene=''>	+	<StructureSection load='4dni' size='340' side='right'caption='[[4dni]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dni]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Trypanosoma_(trypanozoon)_brucei~~ Trypanosoma ~~(trypanozoon)~~ brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DNI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dni]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei] and [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei_TREU927 Trypanosoma brucei brucei TREU927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DNI FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KREPA3, KREPA6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>	+	</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=4dni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dni OCA], [https://pdbe.org/4dni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dni RCSB], [https://www.ebi.ac.uk/pdbsum/4dni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dni 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=4dni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dni OCA], [~~http~~://pdbe.org/4dni PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dni RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dni PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dni ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q38B90_TRYB2 Q38B90_TRYB2]] [[https://www.uniprot.org/uniprot/Q95W13_9TRYP Q95W13_9TRYP]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hol, W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Park, Y J~~]]	+	[[Category: Trypanosoma brucei]]
-	[[Category: ~~Editosome~~]]	+	[[Category: Trypanosoma brucei brucei TREU927]]
-	[[Category: ~~Krepa3~~]]	+	[[Category: Hol W]]
-	[[Category: ~~Krepa6]]~~	+	[[Category: Park Y-J]]
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Protein/rna binding]]~~	+
-	~~[[Category: Rna binding protein~~]]	+

OCA at 02:47, 11 December 2016

2016-12-11T02:47:18Z

←Older revision		Revision as of 02:47, 11 December 2016
Line 1:		Line 1:
		+
	==Structure of Editosome protein==		==Structure of Editosome protein==
	<StructureSection load='4dni' size='340' side='right' caption='[[4dni]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='4dni' size='340' side='right' caption='[[4dni]], [[Resolution\|resolution]] 2.55Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4dni]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DNI FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dni]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DNI FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KREPA3, KREPA6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KREPA3, KREPA6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</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=4dni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dni OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dni RCSB], [http://www.ebi.ac.uk/pdbsum/4dni 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=4dni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dni OCA], [http://pdbe.org/4dni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dni RCSB], [http://www.ebi.ac.uk/pdbsum/4dni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dni ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4dni" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:56, 9 December 2014

2014-12-09T14:56:05Z

←Older revision		Revision as of 14:56, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4dni.~~jpg~~\|~~left\|200px~~]]	+	==Structure of Editosome protein==
		+	<StructureSection load='4dni' size='340' side='right' caption='[[4dni]], [[Resolution\|resolution]] 2.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4dni]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DNI FirstGlance]. <br>
		+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KREPA3, KREPA6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</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=4dni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dni OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dni RCSB], [http://www.ebi.ac.uk/pdbsum/4dni PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trypanosomatids form a group of protozoa which contain parasites of human, animals and plants. Several of these species cause major human diseases, including Trypanosoma brucei which is the causative agent of human African trypanosomiasis, also called sleeping sickness. These organisms have many highly unusual features including a unique U-insertion/deletion RNA editing process in the single mitochondrion. A key multi-protein complex, called the approximately 20S editosome, or editosome, carries out a cascade of essential RNA-modifying reactions and contains a core of 12 different proteins of which six are the interaction proteins A1 to A6. Each of these interaction proteins comprises a C-terminal OB-fold and the smallest interaction protein A6 has been shown to interact with four other editosome OB-folds. Here we report the results of a "linked OB-fold" approach to obtain a view of how multiple OB-folds might interact in the core of the editosome. Constructs with variants of linked domains in 25 expression and co-expression experiments resulted in 13 soluble multi-OB-fold complexes. In several instances, these complexes were more homogeneous in size than those obtained from corresponding unlinked OB-folds. The crystal structure of A3(OB) linked to A6 could be elucidated and confirmed the tight interaction between these two OB domains as seen also in our recent complex of A3(OB) and A6 with nanobodies. In the current crystal structure of A3(OB) linked to A6, hydrophobic side chains reside in well-defined pockets of neighboring OB-fold domains. When analyzing the available crystal structures of editosome OB-folds, it appears that in five instances "Pocket 1" of A1(OB), A3(OB) and A6 is occupied by a hydrophobic side chain from a neighboring protein. In these three different OB-folds, Pocket 1 is formed by two conserved sequence motifs and an invariant arginine. These pockets might play a key role in the assembly or mechanism of the editosome by interacting with hydrophobic side chains from other proteins.

-	~~{{STRUCTURE_4dni\| PDB=4dni \| SCENE= }}~~	+	Explorations of linked editosome domains leading to the discovery of motifs defining conserved pockets in editosome OB-folds.,Park YJ, Hol WG J Struct Biol. 2012 Nov;180(2):362-73. doi: 10.1016/j.jsb.2012.07.012. Epub 2012 , Aug 10. PMID:22902563<ref>PMID:22902563</ref>

-	~~===Structure~~ of ~~Editosome protein===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22902563}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4dni]] is a 1 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA].~~	+	</StructureSection>
-	[[Category: Hol, W.]]	+	[[Category: Hol, W]]
-	[[Category: Park, Y J.]]	+	[[Category: Park, Y J]]
	[[Category: Editosome]]		[[Category: Editosome]]
	[[Category: Krepa3]]		[[Category: Krepa3]]

OCA at 09:22, 2 January 2013

2013-01-02T09:22:54Z

←Older revision		Revision as of 09:22, 2 January 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4dni.jpg\|left\|200px]]

-	~~The entry~~ 4dni ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4dni\| PDB=4dni \| SCENE= }}

-	~~Authors: Park, Y.-J., Hol, W.~~	+	===Structure of Editosome protein===

-	~~Description:~~ Structure of Editosome protein	+	{{ABSTRACT_PUBMED_22902563}}
		+
		+	==About this Structure==
		+	[[4dni]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DNI OCA].
		+	[[Category: Hol, W.]]
		+	[[Category: Park, Y J.]]
		+	[[Category: Editosome]]
		+	[[Category: Krepa3]]
		+	[[Category: Krepa6]]
		+	[[Category: Protein binding]]
		+	[[Category: Protein/rna binding]]
		+	[[Category: Rna binding protein]]

OCA at 07:30, 22 February 2012

2012-02-22T07:30:19Z

←Older revision		Revision as of 07:30, 22 February 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dni is ON HOLD	+	The entry 4dni is ON HOLD until Paper Publication

	Authors: Park, Y.-J., Hol, W.		Authors: Park, Y.-J., Hol, W.

	Description: Structure of Editosome protein		Description: Structure of Editosome protein

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

2012-02-15T06:25:38Z

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

←Older revision

Revision as of 06:25, 15 February 2012

OCA: New page: '''Unreleased structure''' The entry 4dni is ON HOLD Authors: Park, Y.-J., Hol, W. Description: Structure of Editosome protein

2012-02-15T06:25:37Z

New page: '''Unreleased structure''' The entry 4dni is ON HOLD Authors: Park, Y.-J., Hol, W. Description: Structure of Editosome protein

New page

'''Unreleased structure'''

The entry 4dni is ON HOLD

Authors: Park, Y.-J., Hol, W.

Description: Structure of Editosome protein