5nkm - Revision history

OCA at 09:52, 15 November 2023

2023-11-15T09:52:11Z

←Older revision		Revision as of 09:52, 15 November 2023
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	<StructureSection load='5nkm' size='340' side='right'caption='[[5nkm]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='5nkm' size='340' side='right'caption='[[5nkm]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nkm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5NKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nkm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NKM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS~~</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]] 2.493Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=5nkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkm OCA], [~~http~~://pdbe.org/5nkm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nkm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nkm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkm 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=5nkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkm OCA], [https://pdbe.org/5nkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nkm RCSB], [https://www.ebi.ac.uk/pdbsum/5nkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SMG8_CAEEL SMG8_CAEEL]] Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Probable component of kinase complex containing smg-1 and recruited to stalled ribosomes.<ref>PMID:19417104</ref> [[http://www.uniprot.org/uniprot/SMG9_CAEEL SMG9_CAEEL]] Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Probable component of kinase complex containing smg-1 and recruited to stalled ribosomes.<ref>PMID:19417104</ref>	+	[https://www.uniprot.org/uniprot/SMG8_CAEEL SMG8_CAEEL] Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Probable component of kinase complex containing smg-1 and recruited to stalled ribosomes.<ref>PMID:19417104</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caenorhabditis elegans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basquin, J]]	+	[[Category: Basquin J]]
-	[[Category: Conti, E]]	+	[[Category: Conti E]]
-	[[Category: Li, L]]	+	[[Category: Li L]]
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Smg8-smg9 complex nmd effector protein~~]]	+

OCA at 12:06, 26 August 2020

2020-08-26T12:06:46Z

←Older revision		Revision as of 12:06, 26 August 2020
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	==SMG8-SMG9 complex==		==SMG8-SMG9 complex==
-	<StructureSection load='5nkm' size='340' side='right' caption='[[5nkm]], [[Resolution\|resolution]] 2.49Å' scene=''>	+	<StructureSection load='5nkm' size='340' side='right'caption='[[5nkm]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nkm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nkm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NKM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5nkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkm OCA], [http://pdbe.org/5nkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nkm RCSB], [http://www.ebi.ac.uk/pdbsum/5nkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkm 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=5nkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkm OCA], [http://pdbe.org/5nkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nkm RCSB], [http://www.ebi.ac.uk/pdbsum/5nkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Basquin, J]]		[[Category: Basquin, J]]
	[[Category: Conti, E]]		[[Category: Conti, E]]

OCA at 13:02, 19 April 2017

2017-04-19T13:02:56Z

←Older revision		Revision as of 13:02, 19 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nkm is ~~ON HOLD~~	+	==SMG8-SMG9 complex==
		+	<StructureSection load='5nkm' size='340' side='right' caption='[[5nkm]], [[Resolution\|resolution]] 2.49Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5nkm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NKM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5nkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkm OCA], [http://pdbe.org/5nkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nkm RCSB], [http://www.ebi.ac.uk/pdbsum/5nkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SMG8_CAEEL SMG8_CAEEL]] Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Probable component of kinase complex containing smg-1 and recruited to stalled ribosomes.<ref>PMID:19417104</ref> [[http://www.uniprot.org/uniprot/SMG9_CAEEL SMG9_CAEEL]] Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Probable component of kinase complex containing smg-1 and recruited to stalled ribosomes.<ref>PMID:19417104</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA degradation pathway involved in surveillance and post-transcriptional regulation, and executed by the concerted action of several trans-acting factors. The SMG1 kinase is an essential NMD factor in metazoans and is associated with two recently identified and yet poorly characterized proteins, SMG8 and SMG9. We determined the 2.5 A resolution crystal structure of a SMG8-SMG9 core complex from C. elegans. We found that SMG8-SMG9 is a G domain heterodimer with architectural similarities to the dynamin-like family of GTPases such as Atlastin and GBP1. The SMG8-SMG9 heterodimer forms in the absence of nucleotides, with interactions conserved from worms to humans. Nucleotide binding occurs at the G domain of SMG9 but not of SMG8. Fitting the GDP-bound SMG8-SMG9 structure in EM densities of the human SMG1-SMG8-SMG9 complex raises the possibility that the nucleotide site of SMG9 faces SMG1 and could impact on the kinase conformation and/or regulation.

-	~~Authors: Li~~, L., Basquin, J., Conti, E.	+	Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins.,Li L, Lingaraju M, Basquin C, Basquin J, Conti E RNA. 2017 Apr 7. pii: rna.061200.117. doi: 10.1261/rna.061200.117. PMID:28389433<ref>PMID:28389433</ref>

-	~~Description: SMG8-SMG9 complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5nkm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Basquin, J]]		[[Category: Basquin, J]]
-	[[Category: Li, L]]
	[[Category: Conti, E]]		[[Category: Conti, E]]
		+	[[Category: Li, L]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Smg8-smg9 complex nmd effector protein]]

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

2017-04-12T08:05:55Z

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

←Older revision

Revision as of 08:05, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5nkm is ON HOLD Authors: Li, L., Basquin, J., Conti, E. Description: SMG8-SMG9 complex Category: Unreleased Structures Category: Basquin, J...

2017-04-12T08:05:53Z

New page: '''Unreleased structure''' The entry 5nkm is ON HOLD Authors: Li, L., Basquin, J., Conti, E. Description: SMG8-SMG9 complex Category: Unreleased Structures Category: Basquin, J...

New page

'''Unreleased structure'''

The entry 5nkm is ON HOLD

Authors: Li, L., Basquin, J., Conti, E.

Description: SMG8-SMG9 complex
[[Category: Unreleased Structures]]
[[Category: Basquin, J]]
[[Category: Li, L]]
[[Category: Conti, E]]