6f9w: Difference between revisions

Latest revision as of 09:54, 23 October 2024

Crystal structure of the LSM domain of LSM14 in complex with a C-terminal peptide of 4E-T

Structural highlights

6f9w is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.623Å
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LS14A_HUMAN Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs.^[1] ^[2]

Publication Abstract from PubMed

The LSM domain-containing protein LSM14/Rap55 plays a role in mRNA decapping, translational repression, and RNA granule (P-body) assembly. How LSM14 interacts with the mRNA silencing machinery, including the eIF4E-binding protein 4E-T and the DEAD-box helicase DDX6, is poorly understood. Here we report the crystal structure of the LSM domain of LSM14 bound to a highly conserved C-terminal fragment of 4E-T. The 4E-T C-terminus forms a bi-partite motif that wraps around the N-terminal LSM domain of LSM14. We also determined the crystal structure of LSM14 bound to the C-terminal RecA-like domain of DDX6. LSM14 binds DDX6 via a unique non-contiguous motif with distinct directionality as compared to other DDX6-interacting proteins. Together with mutational and proteomic studies, the LSM14-DDX6 structure reveals that LSM14 has adopted a divergent mode of binding DDX6 in order to support the formation of mRNA silencing complexes and P-body assembly.

Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes.,Brandmann T, Fakim H, Padamsi Z, Youn JY, Gingras AC, Fabian MR, Jinek M EMBO J. 2018 Mar 6. pii: embj.201797869. doi: 10.15252/embj.201797869. PMID:29510985^[3]

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

References

↑ Yang WH, Yu JH, Gulick T, Bloch KD, Bloch DB. RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules. RNA. 2006 Apr;12(4):547-54. doi: 10.1261/rna.2302706. Epub 2006 Feb 16. PMID:16484376 doi:https://dx.doi.org/10.1261/rna.2302706
↑ Tanaka KJ, Ogawa K, Takagi M, Imamoto N, Matsumoto K, Tsujimoto M. RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes. J Biol Chem. 2006 Dec 29;281(52):40096-106. doi: 10.1074/jbc.M609059200. Epub, 2006 Oct 30. PMID:17074753 doi:https://dx.doi.org/10.1074/jbc.M609059200
↑ Brandmann T, Fakim H, Padamsi Z, Youn JY, Gingras AC, Fabian MR, Jinek M. Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes. EMBO J. 2018 Mar 6. pii: embj.201797869. doi: 10.15252/embj.201797869. PMID:29510985 doi:https://dx.doi.org/10.15252/embj.201797869

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OCA

[1] Yang WH, Yu JH, Gulick T, Bloch KD, Bloch DB. RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules. RNA. 2006 Apr;12(4):547-54. doi: 10.1261/rna.2302706. Epub 2006 Feb 16. PMID:16484376 doi:https://dx.doi.org/10.1261/rna.2302706

[2] Tanaka KJ, Ogawa K, Takagi M, Imamoto N, Matsumoto K, Tsujimoto M. RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes. J Biol Chem. 2006 Dec 29;281(52):40096-106. doi: 10.1074/jbc.M609059200. Epub, 2006 Oct 30. PMID:17074753 doi:https://dx.doi.org/10.1074/jbc.M609059200

[3] Brandmann T, Fakim H, Padamsi Z, Youn JY, Gingras AC, Fabian MR, Jinek M. Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes. EMBO J. 2018 Mar 6. pii: embj.201797869. doi: 10.15252/embj.201797869. PMID:29510985 doi:https://dx.doi.org/10.15252/embj.201797869

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the LSM domain of LSM14 in complex with a C-terminal peptide of 4E-T==
-<StructureSection load='6f9w' size='340' side='right' caption='[[6f9w]], [[Resolution|resolution]] 2.62&Aring;' scene=''>
+<StructureSection load='6f9w' size='340' side='right'caption='[[6f9w]], [[Resolution|resolution]] 2.62&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6f9w]] 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=6F9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F9W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6f9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F9W FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.623&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LSM14A, C19orf13, FAM61A, RAP55, RAP55A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), EIF4ENIF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=6f9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f9w OCA], [http://pdbe.org/6f9w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f9w RCSB], [http://www.ebi.ac.uk/pdbsum/6f9w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f9w 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=6f9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f9w OCA], [https://pdbe.org/6f9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f9w RCSB], [https://www.ebi.ac.uk/pdbsum/6f9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f9w ProSAT]</span></td></tr>
 </table>
-== Disease ==
-[[http://www.uniprot.org/uniprot/4ET_HUMAN 4ET_HUMAN]] Primary ovarian failure.
 == Function ==
-[[http://www.uniprot.org/uniprot/LS14A_HUMAN LS14A_HUMAN]] Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs.<ref>PMID:16484376</ref> <ref>PMID:17074753</ref>  [[http://www.uniprot.org/uniprot/4ET_HUMAN 4ET_HUMAN]] Nucleoplasmic shuttling protein. Mediates the nuclear import of EIF4E by a piggy-back mechanism.
+[https://www.uniprot.org/uniprot/LS14A_HUMAN LS14A_HUMAN] Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs.<ref>PMID:16484376</ref> <ref>PMID:17074753</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Brandmann, T]]
+[[Category: Large Structures]]
-[[Category: Jinek, M]]
+[[Category: Brandmann T]]
-[[Category: Decapping]]
+[[Category: Jinek M]]
-[[Category: Mrna turnover]]
-[[Category: Rna]]
-[[Category: Translational repression]]

6f9w: Difference between revisions

Latest revision as of 09:54, 23 October 2024

Crystal structure of the LSM domain of LSM14 in complex with a C-terminal peptide of 4E-T

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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