2xzo - Revision history

OCA at 10:42, 20 December 2023

OCA — Wed, 20 Dec 2023 10:42:29 GMT

←Older revision		Revision as of 10:42, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='2xzo' size='340' side='right'caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2xzo' size='340' side='right'caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XZO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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]] 2.395Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [https://pdbe.org/2xzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [https://www.ebi.ac.uk/pdbsum/2xzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzo 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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [https://pdbe.org/2xzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [https://www.ebi.ac.uk/pdbsum/2xzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RENT1_HUMAN RENT1_HUMAN]] RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.<ref>PMID:11163187</ref> <ref>PMID:16086026</ref> <ref>PMID:18172165</ref> <ref>PMID:21145460</ref> <ref>PMID:21419344</ref>	+	[https://www.uniprot.org/uniprot/RENT1_HUMAN RENT1_HUMAN] RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.<ref>PMID:11163187</ref> <ref>PMID:16086026</ref> <ref>PMID:18172165</ref> <ref>PMID:21145460</ref> <ref>PMID:21419344</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RNA helicase~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Basquin, C]]	+	[[Category: Basquin C]]
-	[[Category: Bonneau, F]]	+	[[Category: Bonneau F]]
-	[[Category: Chakrabarti, S]]	+	[[Category: Chakrabarti S]]
-	[[Category: Conti, E]]	+	[[Category: Conti E]]
-	[[Category: Domcke, S]]	+	[[Category: Domcke S]]
-	[[Category: Fiorini, F]]	+	[[Category: Fiorini F]]
-	~~[[Category: Hir, H Le~~]]	+	[[Category: Jayachandran U]]
-	[[Category: Jayachandran, U]]	+	[[Category: Le Hir H]]
-	[[Category: ~~Allosteric regulation]]~~	+
-	~~[[Category: Hydrolase-rna complex]]~~	+
-	~~[[Category: Nmd]]~~	+
-	~~[[Category: Rna degradation~~]]	+

OCA at 12:20, 27 April 2022

OCA — Wed, 27 Apr 2022 12:20:39 GMT

←Older revision		Revision as of 12:20, 27 April 2022
Line 3:		Line 3:
	<StructureSection load='2xzo' size='340' side='right'caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2xzo' size='340' side='right'caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2XZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XZO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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">[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [~~http~~://pdbe.org/2xzo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2xzo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzo 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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [https://pdbe.org/2xzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [https://www.ebi.ac.uk/pdbsum/2xzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RENT1_HUMAN RENT1_HUMAN]] RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.<ref>PMID:11163187</ref> <ref>PMID:16086026</ref> <ref>PMID:18172165</ref> <ref>PMID:21145460</ref> <ref>PMID:21419344</ref>	+	[[https://www.uniprot.org/uniprot/RENT1_HUMAN RENT1_HUMAN]] RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.<ref>PMID:11163187</ref> <ref>PMID:16086026</ref> <ref>PMID:18172165</ref> <ref>PMID:21145460</ref> <ref>PMID:21419344</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:28, 22 July 2020

OCA — Wed, 22 Jul 2020 12:28:24 GMT

←Older revision		Revision as of 12:28, 22 July 2020
Line 1:		Line 1:

	==Upf1 helicase - RNA complex==		==Upf1 helicase - RNA complex==
-	<StructureSection load='2xzo' size='340' side='right' caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='2xzo' size='340' side='right'caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2XZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XZO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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">[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [http://pdbe.org/2xzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [http://www.ebi.ac.uk/pdbsum/2xzo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzo ProSAT]</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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [http://pdbe.org/2xzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [http://www.ebi.ac.uk/pdbsum/2xzo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Helicase\|Helicase]]	+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Basquin, C]]		[[Category: Basquin, C]]

OCA at 09:32, 10 October 2018

OCA — Wed, 10 Oct 2018 09:32:47 GMT

←Older revision		Revision as of 09:32, 10 October 2018
Line 1:		Line 1:

-	==~~UPF1 HELICASE~~ - RNA ~~COMPLEX~~==	+	==Upf1 helicase - RNA complex==
	<StructureSection load='2xzo' size='340' side='right' caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2xzo' size='340' side='right' caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 17:57, 5 August 2016

OCA — Fri, 05 Aug 2016 17:57:20 GMT

←Older revision		Revision as of 17:57, 5 August 2016
Line 1:		Line 1:
		+
	==UPF1 HELICASE - RNA COMPLEX==		==UPF1 HELICASE - RNA COMPLEX==
	<StructureSection load='2xzo' size='340' side='right' caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2xzo' size='340' side='right' caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XZO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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">[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [http://www.ebi.ac.uk/pdbsum/2xzo 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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [http://pdbe.org/2xzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [http://www.ebi.ac.uk/pdbsum/2xzo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 2xzo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Basquin, C]]		[[Category: Basquin, C]]

OCA at 20:48, 25 December 2014

OCA — Thu, 25 Dec 2014 20:48:04 GMT

←Older revision		Revision as of 20:48, 25 December 2014
Line 8:		Line 8:
	<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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [http://www.ebi.ac.uk/pdbsum/2xzo 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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [http://www.ebi.ac.uk/pdbsum/2xzo PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RENT1_HUMAN RENT1_HUMAN]] RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.<ref>PMID:11163187</ref> <ref>PMID:16086026</ref> <ref>PMID:18172165</ref> <ref>PMID:21145460</ref> <ref>PMID:21419344</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 27:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
-	[[Category: Basquin, C.]]	+	[[Category: Basquin, C]]
-	[[Category: Bonneau, F.]]	+	[[Category: Bonneau, F]]
-	[[Category: Chakrabarti, S.]]	+	[[Category: Chakrabarti, S]]
-	[[Category: Conti, E.]]	+	[[Category: Conti, E]]
-	[[Category: Domcke, S.]]	+	[[Category: Domcke, S]]
-	[[Category: Fiorini, F.]]	+	[[Category: Fiorini, F]]
-	[[Category: Hir, H Le.]]	+	[[Category: Hir, H Le]]
-	[[Category: Jayachandran, U.]]	+	[[Category: Jayachandran, U]]
	[[Category: Allosteric regulation]]		[[Category: Allosteric regulation]]
	[[Category: Hydrolase-rna complex]]		[[Category: Hydrolase-rna complex]]
	[[Category: Nmd]]		[[Category: Nmd]]
	[[Category: Rna degradation]]		[[Category: Rna degradation]]

OCA at 13:14, 22 October 2014

OCA — Wed, 22 Oct 2014 13:14:45 GMT

←Older revision		Revision as of 13:14, 22 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2xzo.~~png~~\|~~left~~\|~~200px~~]]	+	==UPF1 HELICASE - RNA COMPLEX==
		+	<StructureSection load='2xzo' size='340' side='right' caption='[[2xzo]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XZO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</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">[[2wjv\|2wjv]], [[2wjy\|2wjy]], [[2iyk\|2iyk]], [[2xzp\|2xzp]], [[2gjk\|2gjk]], [[2gk7\|2gk7]], [[2gk6\|2gk6]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=2xzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xzo RCSB], [http://www.ebi.ac.uk/pdbsum/2xzo PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Upf1 is a crucial factor in nonsense-mediated mRNA decay, the eukaryotic surveillance pathway that degrades mRNAs containing premature stop codons. The essential RNA-dependent ATPase activity of Upf1 is triggered by the formation of the surveillance complex with Upf2-Upf3. We report crystal structures of Upf1 in the presence and absence of the CH domain, captured in the transition state with ADP:AlF(4)(-) and RNA. In isolation, Upf1 clamps onto the RNA, enclosing it in a channel formed by both the catalytic and regulatory domains. Upon binding to Upf2, the regulatory CH domain of Upf1 undergoes a large conformational change, causing the catalytic helicase domain to bind RNA less extensively and triggering its helicase activity. Formation of the surveillance complex thus modifies the RNA binding properties and the catalytic activity of Upf1, causing it to switch from an RNA-clamping mode to an RNA-unwinding mode.

-	~~{{STRUCTURE_2xzo\| PDB=2xzo \| SCENE= }}~~	+	Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2.,Chakrabarti S, Jayachandran U, Bonneau F, Fiorini F, Basquin C, Domcke S, Le Hir H, Conti E Mol Cell. 2011 Mar 18;41(6):693-703. PMID:21419344<ref>PMID:21419344</ref>

-	~~===UPF1 HELICASE - RNA COMPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21419344}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2xzo]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA].~~	+

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021419344<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]

OCA at 21:26, 20 October 2012

OCA — Sat, 20 Oct 2012 21:26:59 GMT

←Older revision		Revision as of 21:26, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2xzo]] is a 2 chain structure ~~of [[Helicase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA].	+	[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA].

	==See Also==		==See Also==

OCA at 13:17, 27 July 2012

OCA — Fri, 27 Jul 2012 13:17:22 GMT

←Older revision		Revision as of 13:17, 27 July 2012
Line 1:		Line 1:
-	[[Image:2xzo.~~jpg~~\|left\|200px]]	+	[[Image:2xzo.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2xzo", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2xzo\| PDB=2xzo \| SCENE= }}		{{STRUCTURE_2xzo\| PDB=2xzo \| SCENE= }}

	===UPF1 HELICASE - RNA COMPLEX===		===UPF1 HELICASE - RNA COMPLEX===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21419344}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21419344 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21419344}}		{{ABSTRACT_PUBMED_21419344}}

	==About this Structure==		==About this Structure==
-	[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA].	+	[[2xzo]] is a 2 chain structure of [[Helicase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA].
		+
		+	==See Also==
		+	*[[Helicase\|Helicase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21419344~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021419344</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
Line 33:		Line 25:
	[[Category: Hir, H Le.]]		[[Category: Hir, H Le.]]
	[[Category: Jayachandran, U.]]		[[Category: Jayachandran, U.]]
		+	[[Category: Allosteric regulation]]
		+	[[Category: Hydrolase-rna complex]]
		+	[[Category: Nmd]]
		+	[[Category: Rna degradation]]

OCA at 08:05, 30 March 2011

OCA — Wed, 30 Mar 2011 08:05:42 GMT

←Older revision		Revision as of 08:05, 30 March 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:2xzo.jpg\|left\|200px]]

-	The ~~entry 2xzo~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2xzo", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_2xzo\| PDB=2xzo \| SCENE= }}

-	~~Authors: Chakrabarti, S., Jayachandran, U., Bonneau, F., Fiorini, F., Basquin, C., Domcke, S., Le Hir, H., Conti, E.~~	+	===UPF1 HELICASE - RNA COMPLEX===

-	~~Description~~: ~~Upf1 helicase~~ -RNA ~~complex~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21419344}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21419344 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21419344}}
		+
		+	==About this Structure==
		+	[[2xzo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZO OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21419344</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: RNA helicase]]
		+	[[Category: Basquin, C.]]
		+	[[Category: Bonneau, F.]]
		+	[[Category: Chakrabarti, S.]]
		+	[[Category: Conti, E.]]
		+	[[Category: Domcke, S.]]
		+	[[Category: Fiorini, F.]]
		+	[[Category: Hir, H Le.]]
		+	[[Category: Jayachandran, U.]]