5j3t - Revision history

OCA at 10:44, 6 September 2023

OCA — Wed, 06 Sep 2023 10:44:27 GMT

←Older revision		Revision as of 10:44, 6 September 2023
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	<StructureSection load='5j3t' size='340' side='right'caption='[[5j3t]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5j3t' size='340' side='right'caption='[[5j3t]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3t]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cbs_356 Cbs 356~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3t]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J3T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5j3q\|5j3q]], [[5j3y\|5j3y~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dcp1, SPBC3B9.21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4896 CBS 356]), dcp2, SPAC19A8.12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=5j3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3t OCA], [https://pdbe.org/5j3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j3t RCSB], [https://www.ebi.ac.uk/pdbsum/5j3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3t ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/5'-(N(7)-methylguanosine_5'-triphospho)-[mRNA]_hydrolase 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.62 3.6.1.62] </~~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=5j3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3t OCA], [~~http~~://pdbe.org/5j3t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j3t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j3t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3t ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO]] Component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:15671491</ref> [[http://www.uniprot.org/uniprot/DCP2_SCHPO DCP2_SCHPO]] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:15671491</ref>	+	[https://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO] Component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:15671491</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cbs 356]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang~~, C T~~]]	+	[[Category: Schizosaccharomyces pombe]]
-	[[Category: Izaurralde, E]]	+	[[Category: Chang CT]]
-	[[Category: Jonas, S]]	+	[[Category: Izaurralde E]]
-	[[Category: Muthukumar, S]]	+	[[Category: Jonas S]]
-	[[Category: Valkov, E]]	+	[[Category: Muthukumar S]]
-	[[Category: Weichenrieder, O]]	+	[[Category: Valkov E]]
-	~~[[Category: Decapping]]~~	+	[[Category: Weichenrieder O]]
-	~~[[Category: Evh1]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mrna decay]]~~	+
-	~~[[Category: Nudix~~]]	+

OCA at 07:28, 10 June 2020

OCA — Wed, 10 Jun 2020 07:28:11 GMT

←Older revision		Revision as of 07:28, 10 June 2020
Line 1:		Line 1:

	==Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex==		==Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex==
-	<StructureSection load='5j3t' size='340' side='right' caption='[[5j3t]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5j3t' size='340' side='right'caption='[[5j3t]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3T OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3t]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J3T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j3q\|5j3q]], [[5j3y\|5j3y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j3q\|5j3q]], [[5j3y\|5j3y]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dcp1, SPBC3B9.21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356]), dcp2, SPAC19A8.12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-(N(7)-methylguanosine_5'-triphospho)-[mRNA]_hydrolase 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.62 3.6.1.62] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-(N(7)-methylguanosine_5'-triphospho)-[mRNA]_hydrolase 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.62 3.6.1.62] </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=5j3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3t OCA], [http://pdbe.org/5j3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3t RCSB], [http://www.ebi.ac.uk/pdbsum/5j3t PDBsum]</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=5j3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3t OCA], [http://pdbe.org/5j3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3t RCSB], [http://www.ebi.ac.uk/pdbsum/5j3t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cbs 356]]
		+	[[Category: Large Structures]]
	[[Category: Chang, C T]]		[[Category: Chang, C T]]
	[[Category: Izaurralde, E]]		[[Category: Izaurralde, E]]

OCA at 07:24, 1 June 2016

OCA — Wed, 01 Jun 2016 07:24:29 GMT

←Older revision		Revision as of 07:24, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j3t is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex==
		+	<StructureSection load='5j3t' size='340' side='right' caption='[[5j3t]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5j3t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j3q\|5j3q]], [[5j3y\|5j3y]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-(N(7)-methylguanosine_5'-triphospho)-[mRNA]_hydrolase 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.62 3.6.1.62] </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=5j3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3t OCA], [http://pdbe.org/5j3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3t RCSB], [http://www.ebi.ac.uk/pdbsum/5j3t PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO]] Component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:15671491</ref> [[http://www.uniprot.org/uniprot/DCP2_SCHPO DCP2_SCHPO]] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:15671491</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The removal of the mRNA 5' cap (decapping) by Dcp2 shuts down translation and commits mRNA to full degradation. Dcp2 activity is enhanced by activator proteins such as Dcp1 and Edc1. However, owing to conformational flexibility, the active conformation of Dcp2 and the mechanism of decapping activation have remained unknown. Here, we report a 1.6-A-resolution crystal structure of the Schizosaccharomyces pombe Dcp2-Dcp1 heterodimer in an unprecedented conformation that is tied together by an intrinsically disordered peptide from Edc1. In this ternary complex, an unforeseen rotation of the Dcp2 catalytic domain allows residues from both Dcp2 and Dcp1 to cooperate in RNA binding, thus explaining decapping activation by increased substrate affinity. The architecture of the Dcp2-Dcp1-Edc1 complex provides a rationale for the conservation of a sequence motif in Edc1 that is also present in unrelated decapping activators, thus indicating that the presently described mechanism of decapping activation is evolutionarily conserved.

-	~~Authors~~:	+	Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation.,Valkov E, Muthukumar S, Chang CT, Jonas S, Weichenrieder O, Izaurralde E Nat Struct Mol Biol. 2016 May 16. doi: 10.1038/nsmb.3232. PMID:27183195<ref>PMID:27183195</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5j3t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chang, C T]]
		+	[[Category: Izaurralde, E]]
		+	[[Category: Jonas, S]]
		+	[[Category: Muthukumar, S]]
		+	[[Category: Valkov, E]]
		+	[[Category: Weichenrieder, O]]
		+	[[Category: Decapping]]
		+	[[Category: Evh1]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mrna decay]]
		+	[[Category: Nudix]]

OCA at 15:01, 15 May 2016

OCA — Sun, 15 May 2016 15:01:33 GMT

←Older revision		Revision as of 15:01, 15 May 2016
Line 3:		Line 3:
	The entry 5j3t is ON HOLD until Paper Publication		The entry 5j3t is ON HOLD until Paper Publication

-	Authors: ~~Valkov, E., Muthukumar, S., Chang, C.T., Jonas, S., Weichenrieder, O., Izaurralde, E.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Muthukumar, S]]
-	[[Category: Chang, C.T]]
-	[[Category: Izaurralde, E]]
-	[[Category: Weichenrieder, O]]
-	[[Category: Valkov, E]]
-	[[Category: Jonas, S]]

OCA: Protected "5j3t" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:24:42 GMT

Protected "5j3t" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:24, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j3t is ON HOLD until Paper Publication Authors: Valkov, E., Muthukumar, S., Chang, C.T., Jonas, S., Weichenrieder, O., Izaurralde, E. Description:...

OCA — Wed, 11 May 2016 01:24:41 GMT

New page: '''Unreleased structure''' The entry 5j3t is ON HOLD until Paper Publication Authors: Valkov, E., Muthukumar, S., Chang, C.T., Jonas, S., Weichenrieder, O., Izaurralde, E. Description:...

New page

'''Unreleased structure'''

The entry 5j3t is ON HOLD until Paper Publication

Authors: Valkov, E., Muthukumar, S., Chang, C.T., Jonas, S., Weichenrieder, O., Izaurralde, E.

Description:
[[Category: Unreleased Structures]]
[[Category: Muthukumar, S]]
[[Category: Chang, C.T]]
[[Category: Izaurralde, E]]
[[Category: Weichenrieder, O]]
[[Category: Valkov, E]]
[[Category: Jonas, S]]