5nkk - Revision history

OCA at 13:03, 15 November 2023

OCA — Wed, 15 Nov 2023 13:03:07 GMT

←Older revision		Revision as of 13:03, 15 November 2023
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	<StructureSection load='5nkk' size='340' side='right'caption='[[5nkk]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='5nkk' size='340' side='right'caption='[[5nkk]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nkk]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caeel Caeel~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nkk]] 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=5NKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NKK 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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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]] 2.64Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">smg-8, K04B12.3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL]), smg-9, Y54E2A.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=5nkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkk OCA], [~~http~~://pdbe.org/5nkk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nkk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nkk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkk 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=5nkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkk OCA], [https://pdbe.org/5nkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nkk RCSB], [https://www.ebi.ac.uk/pdbsum/5nkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkk 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: ~~Caeel~~]]	+	[[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: Nmd effector protein]]~~	+
-	~~[[Category: Smg8-smg9 complex]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 06:45, 16 October 2019

OCA — Wed, 16 Oct 2019 06:45:42 GMT

←Older revision		Revision as of 06:45, 16 October 2019
Line 1:		Line 1:

	==SMG8-SMG9 complex GDP bound==		==SMG8-SMG9 complex GDP bound==
-	<StructureSection load='5nkk' size='340' side='right' caption='[[5nkk]], [[Resolution\|resolution]] 2.64Å' scene=''>	+	<StructureSection load='5nkk' size='340' side='right'caption='[[5nkk]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nkk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nkk]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NKK 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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>		</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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">smg-8, K04B12.3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL]), smg-9, Y54E2A.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=5nkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkk OCA], [http://pdbe.org/5nkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nkk RCSB], [http://www.ebi.ac.uk/pdbsum/5nkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkk 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=5nkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkk OCA], [http://pdbe.org/5nkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nkk RCSB], [http://www.ebi.ac.uk/pdbsum/5nkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkk ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caeel]]
		+	[[Category: Large Structures]]
	[[Category: Basquin, J]]		[[Category: Basquin, J]]
	[[Category: Conti, E]]		[[Category: Conti, E]]

OCA at 13:02, 19 April 2017

OCA — Wed, 19 Apr 2017 13:02:44 GMT

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

-	~~The entry~~ 5nkk is ~~ON HOLD~~	+	==SMG8-SMG9 complex GDP bound==
		+	<StructureSection load='5nkk' size='340' side='right' caption='[[5nkk]], [[Resolution\|resolution]] 2.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5nkk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NKK 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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=5nkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nkk OCA], [http://pdbe.org/5nkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nkk RCSB], [http://www.ebi.ac.uk/pdbsum/5nkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nkk 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 GDP bound~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5nkk" 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: Nmd effector protein]]
		+	[[Category: Smg8-smg9 complex]]
		+	[[Category: Transcription]]

OCA at 08:05, 12 April 2017

OCA — Wed, 12 Apr 2017 08:05:46 GMT

←Older revision		Revision as of 08:05, 12 April 2017
Line 3:		Line 3:
	The entry 5nkk is ON HOLD		The entry 5nkk is ON HOLD

-	Authors: ~~Liang~~ Li, ~~Jerome~~ Basquin, ~~Elena~~ Conti	+	Authors: Li, L., Basquin, J., Conti, E.

	Description: SMG8-SMG9 complex GDP bound		Description: SMG8-SMG9 complex GDP bound
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Liang Li, Jerome~~ Basquin, ~~Elena~~ Conti]]	+	[[Category: Basquin, J]]
		+	[[Category: Li, L]]
		+	[[Category: Conti, E]]

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

OCA — Wed, 05 Apr 2017 10:15:45 GMT

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

←Older revision

Revision as of 10:15, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5nkk is ON HOLD Authors: Liang Li, Jerome Basquin, Elena Conti Description: SMG8-SMG9 complex GDP bound Category: Unreleased Structures [[Categ...

OCA — Wed, 05 Apr 2017 10:15:44 GMT

New page: '''Unreleased structure''' The entry 5nkk is ON HOLD Authors: Liang Li, Jerome Basquin, Elena Conti Description: SMG8-SMG9 complex GDP bound Category: Unreleased Structures [[Categ...

New page

'''Unreleased structure'''

The entry 5nkk is ON HOLD

Authors: Liang Li, Jerome Basquin, Elena Conti

Description: SMG8-SMG9 complex GDP bound
[[Category: Unreleased Structures]]
[[Category: Liang Li, Jerome Basquin, Elena Conti]]