6o7z - Revision history

OCA at 14:50, 13 March 2024

2024-03-13T14:50:59Z

←Older revision		Revision as of 14:50, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6o7z' size='340' side='right'caption='[[6o7z]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6o7z' size='340' side='right'caption='[[6o7z]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o7z]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Trycr Trycr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o7z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O7Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LRP:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(R)-({(2R,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-3-hydroxy-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium'>LRP</scene>, <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]] 2.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6o7y\|6o7y]], [[6o80\|6o80]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LRP:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(R)-({(2R,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-3-hydroxy-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium'>LRP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">C4B63_13g194 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])~~</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=6o7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7z OCA], [https://pdbe.org/6o7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o7z RCSB], [https://www.ebi.ac.uk/pdbsum/6o7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7z 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=6o7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7z OCA], [~~http~~://pdbe.org/6o7z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o7z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o7z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7z ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A2V2VRR6_TRYCR A0A2V2VRR6_TRYCR]
-	Association of the initiation factor eIF4E with the mRNA cap structure is a key step for translation. Trypanosomatids present six eIF4E homologues, showing a low conservation and also differing significantly from the IF4Es of multicellular eukaryotes. On the mRNA side, while in most eukaryotes the mRNA contains cap-0 (7-methyl-GTP), the trypanosomatid mRNA features a cap-4, which is formed by a cap-0, followed by the AACU sequence containing 2'-O-ribose methylations and base methylations on nucleotides 1 and 4. The studies on eIF4E-cap-4 interaction have been hindered by the difficulty to synthesize this rather elaborated cap-4 sequence. To overcome this problem, we applied a liquid-phase oligonucleotide synthesis strategy and describe for the first time the crystal structure of a trypanosomatid eIF4E (T. cruzi EIF4E5) in complex with cap-4. The TcEIF4E5-cap-4 structure allowed a detailed description of the binding mechanism, revealing the interaction mode for the AACU sequence, with the bases packed in a parallel stacking conformation and involved, together with the methyl groups, in hydrophobic contacts with the protein. This binding mechanism evidences a distinct cap interaction mode in comparison with previously described eIF4E structures and may account for the difference of TcEIF4E5-cap-4 dissociation constant in comparison with other eIF4E homologues.	+
-		+
-	Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4.,Reolon LW, Vichier-Guerre S, de Matos BM, Dugue L, Assuncao TRDS, Tonin Zanchin NI, Pochet S, Guimaraes BG Nucleic Acids Res. 2019 May 8. pii: ~~5486744. doi: 10.1093~~/~~nar~~/~~gkz339~~. ~~PMID:31066441<ref>PMID:31066441</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.~~S. National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6o7z" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Trycr~~]]	+	[[Category: Trypanosoma cruzi]]
-	[[Category: Guimaraes~~, B G~~]]	+	[[Category: Guimaraes BG]]
-	[[Category: Reolon~~, L W]]~~	+	[[Category: Reolon LW]]
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Translation initiation factor~~]]	+

OCA at 07:39, 23 May 2019

2019-05-23T07:39:18Z

←Older revision		Revision as of 07:39, 23 May 2019
Line 3:		Line 3:
	<StructureSection load='6o7z' size='340' side='right'caption='[[6o7z]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6o7z' size='340' side='right'caption='[[6o7z]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o7z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o7z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trycr Trycr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LRP:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(R)-({(2R,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-3-hydroxy-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium'>LRP</scene>, <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"><scene name='pdbligand=LRP:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(R)-({(2R,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-3-hydroxy-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium'>LRP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6o7y\|6o7y]], [[6o80\|6o80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6o7y\|6o7y]], [[6o80\|6o80]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">C4B63_13g194 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</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=6o7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7z OCA], [http://pdbe.org/6o7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7z RCSB], [http://www.ebi.ac.uk/pdbsum/6o7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7z 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=6o7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7z OCA], [http://pdbe.org/6o7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7z RCSB], [http://www.ebi.ac.uk/pdbsum/6o7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7z ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Association of the initiation factor eIF4E with the mRNA cap structure is a key step for translation. Trypanosomatids present six eIF4E homologues, showing a low conservation and also differing significantly from the IF4Es of multicellular eukaryotes. On the mRNA side, while in most eukaryotes the mRNA contains cap-0 (7-methyl-GTP), the trypanosomatid mRNA features a cap-4, which is formed by a cap-0, followed by the AACU sequence containing 2'-O-ribose methylations and base methylations on nucleotides 1 and 4. The studies on eIF4E-cap-4 interaction have been hindered by the difficulty to synthesize this rather elaborated cap-4 sequence. To overcome this problem, we applied a liquid-phase oligonucleotide synthesis strategy and describe for the first time the crystal structure of a trypanosomatid eIF4E (T. cruzi EIF4E5) in complex with cap-4. The TcEIF4E5-cap-4 structure allowed a detailed description of the binding mechanism, revealing the interaction mode for the AACU sequence, with the bases packed in a parallel stacking conformation and involved, together with the methyl groups, in hydrophobic contacts with the protein. This binding mechanism evidences a distinct cap interaction mode in comparison with previously described eIF4E structures and may account for the difference of TcEIF4E5-cap-4 dissociation constant in comparison with other eIF4E homologues.
		+
		+	Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4.,Reolon LW, Vichier-Guerre S, de Matos BM, Dugue L, Assuncao TRDS, Tonin Zanchin NI, Pochet S, Guimaraes BG Nucleic Acids Res. 2019 May 8. pii: 5486744. doi: 10.1093/nar/gkz339. PMID:31066441<ref>PMID:31066441</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6o7z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Trycr]]
	[[Category: Guimaraes, B G]]		[[Category: Guimaraes, B G]]
	[[Category: Reolon, L W]]		[[Category: Reolon, L W]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]
	[[Category: Translation initiation factor]]		[[Category: Translation initiation factor]]

OCA at 08:55, 1 May 2019

2019-05-01T08:55:45Z

←Older revision		Revision as of 08:55, 1 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6o7z is ~~ON HOLD until Paper Publication~~	+	==Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-1==
-		+	<StructureSection load='6o7z' size='340' side='right'caption='[[6o7z]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~Authors~~: ~~Guimaraes~~, B.G., ~~Reolon~~, L.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6o7z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7Z FirstGlance]. <br>
-	~~Description~~: ~~Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap~~-1	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LRP:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(R)-({(2R,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-3-hydroxy-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium'>LRP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6o7y\|6o7y]], [[6o80\|6o80]]</td></tr>
-	[[Category: Reolon, L.W]]	+	<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=6o7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7z OCA], [http://pdbe.org/6o7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7z RCSB], [http://www.ebi.ac.uk/pdbsum/6o7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7z ProSAT]</span></td></tr>
-	[[Category: ~~Guimaraes, B.G~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Guimaraes, B G]]
		+	[[Category: Reolon, L W]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Translation initiation factor]]

OCA at 04:35, 3 April 2019

2019-04-03T04:35:15Z

←Older revision		Revision as of 04:35, 3 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o7z is ON HOLD	+	The entry 6o7z is ON HOLD until Paper Publication

	Authors: Guimaraes, B.G., Reolon, L.W.		Authors: Guimaraes, B.G., Reolon, L.W.

OCA: Protected "6o7z" [edit=sysop:move=sysop]

2019-03-20T05:57:48Z

Protected "6o7z" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:57, 20 March 2019

OCA: New page: '''Unreleased structure''' The entry 6o7z is ON HOLD Authors: Guimaraes, B.G., Reolon, L.W. Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-1 [[...

2019-03-20T05:57:46Z

New page: '''Unreleased structure''' The entry 6o7z is ON HOLD Authors: Guimaraes, B.G., Reolon, L.W. Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-1 [[...

New page

'''Unreleased structure'''

The entry 6o7z is ON HOLD

Authors: Guimaraes, B.G., Reolon, L.W.

Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-1
[[Category: Unreleased Structures]]
[[Category: Reolon, L.W]]
[[Category: Guimaraes, B.G]]