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5nkm

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SMG8-SMG9 complex

Structural highlights

5nkm is a 6 chain structure with sequence from Caenorhabditis elegans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.493Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yamashita A, Izumi N, Kashima I, Ohnishi T, Saari B, Katsuhata Y, Muramatsu R, Morita T, Iwamatsu A, Hachiya T, Kurata R, Hirano H, Anderson P, Ohno S. SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. Genes Dev. 2009 May 1;23(9):1091-105. PMID:19417104 doi:http://dx.doi.org/23/9/1091
↑ Li L, Lingaraju M, Basquin C, Basquin J, Conti E. Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins. RNA. 2017 Apr 7. pii: rna.061200.117. doi: 10.1261/rna.061200.117. PMID:28389433 doi:http://dx.doi.org/10.1261/rna.061200.117

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5nkm"

Categories: Caenorhabditis elegans | Large Structures | Basquin J | Conti E | Li L

@@ Line 3: / Line 3: @@
 <StructureSection load='5nkm' size='340' side='right'caption='[[5nkm]], [[Resolution|resolution]] 2.49&Aring;' 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://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]] 2.493&#8491;</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>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Caenorhabditis elegans]]
 [[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]]

5nkm

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Current revision

SMG8-SMG9 complex

Structural highlights

Function

Publication Abstract from PubMed

References

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