6o7y - Revision history

OCA at 14:50, 13 March 2024

2024-03-13T14:50:57Z

← Older revision		Revision as of 14:50, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6o7y' size='340' side='right'caption='[[6o7y]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6o7y' size='340' side='right'caption='[[6o7y]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6o7y]] 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=6O7Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O7Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[6o7y]] 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=6O7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O7Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LRM:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-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-3H-purin-7-ium'>LRM</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]] 2.2Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6o80\|6o80]], [[6o7z\|6o7z]]</td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LRM:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-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-3H-purin-7-ium'>LRM</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=6o7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7y OCA], [https://pdbe.org/6o7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o7y RCSB], [https://www.ebi.ac.uk/pdbsum/6o7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7y 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=6o7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7y OCA], [~~http~~://pdbe.org/6o7y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o7y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o7y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7y 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 6o7y" 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: Cap-4]]~~
	~~[[Category: Rna binding protein]]~~
	~~[[Category: Translation initiation factor]]~~
	~~[[Category: Trypanosomatid~~]]

OCA at 07:39, 23 May 2019

2019-05-23T07:39:16Z

← Older revision		Revision as of 07:39, 23 May 2019
Line 3:		Line 3:
	<StructureSection load='6o7y' size='340' side='right'caption='[[6o7y]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6o7y' size='340' side='right'caption='[[6o7y]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6o7y]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[6o7y]] 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=6O7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LRM:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-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-3H-purin-7-ium'>LRM</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=LRM:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-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-3H-purin-7-ium'>LRM</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">[[6o80\|6o80]], [[6o7z\|6o7z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6o80\|6o80]], [[6o7z\|6o7z]]</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=6o7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7y OCA], [http://pdbe.org/6o7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7y RCSB], [http://www.ebi.ac.uk/pdbsum/6o7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7y 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=6o7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7y OCA], [http://pdbe.org/6o7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7y RCSB], [http://www.ebi.ac.uk/pdbsum/6o7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7y 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 6o7y" 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]]

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~~ 6o7y is ~~ON HOLD~~		==Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-4==
			<StructureSection load='6o7y' size='340' side='right'caption='[[6o7y]], [[Resolution\|resolution]] 2.20Å' scene=''>
	~~Authors~~: ~~Guimaraes~~, B.G., ~~Reolon~~, L.W.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6o7y]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7Y FirstGlance]. <br>
	~~Description~~: ~~Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-4~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LRM:2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-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-3H-purin-7-ium'>LRM</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">[[6o80\|6o80]], [[6o7z\|6o7z]]</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=6o7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7y OCA], [http://pdbe.org/6o7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7y RCSB], [http://www.ebi.ac.uk/pdbsum/6o7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7y ProSAT]</span></td></tr>
	[[Category: ~~Guimaraes, B.G~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Guimaraes, B G]]
			[[Category: Reolon, L W]]
			[[Category: Cap-4]]
			[[Category: Rna binding protein]]
			[[Category: Translation initiation factor]]
			[[Category: Trypanosomatid]]

OCA at 04:52, 24 April 2019

2019-04-24T04:52:22Z

← Older revision		Revision as of 04:52, 24 April 2019
Line 5:		Line 5:
	Authors: Guimaraes, B.G., Reolon, L.W.		Authors: Guimaraes, B.G., Reolon, L.W.

	Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with ~~cap4~~		Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-4
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Reolon, L.W]]		[[Category: Reolon, L.W]]
	[[Category: Guimaraes, B.G]]		[[Category: Guimaraes, B.G]]

OCA: Protected "6o7y" [edit=sysop:move=sysop]

2019-03-20T05:57:37Z

Protected "6o7y" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:57, 20 March 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6o7y is ON HOLD Authors: Guimaraes, B.G., Reolon, L.W. Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap4 [[C...

2019-03-20T05:57:36Z

New page: '''Unreleased structure''' The entry 6o7y is ON HOLD Authors: Guimaraes, B.G., Reolon, L.W. Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap4 [[C...

New page

'''Unreleased structure'''

The entry 6o7y is ON HOLD

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

Description: Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap4
[[Category: Unreleased Structures]]
[[Category: Reolon, L.W]]
[[Category: Guimaraes, B.G]]