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5k4b

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==Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 1==
==Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 1==
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<StructureSection load='5k4b' size='340' side='right' caption='[[5k4b]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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<StructureSection load='5k4b' size='340' side='right'caption='[[5k4b]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5k4b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K4B FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5k4b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nasonia_vitripennis Nasonia vitripennis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K4B FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.399&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k4c|5k4c]], [[5k4d|5k4d]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
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<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=5k4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4b OCA], [http://pdbe.org/5k4b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k4b RCSB], [http://www.ebi.ac.uk/pdbsum/5k4b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4b ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5k4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4b OCA], [https://pdbe.org/5k4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k4b RCSB], [https://www.ebi.ac.uk/pdbsum/5k4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/K7IM66_NASVI K7IM66_NASVI]] Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.[HAMAP-Rule:MF_03003]
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[https://www.uniprot.org/uniprot/EIF3D_NASVI EIF3D_NASVI] mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. In the eIF-3 complex, eif3d specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs.[HAMAP-Rule:MF_03003]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Eukaryotic mRNAs contain a 5' cap structure that is crucial for recruitment of the translation machinery and initiation of protein synthesis. mRNA recognition is thought to require direct interactions between eukaryotic initiation factor 4E (eIF4E) and the mRNA cap. However, translation of numerous capped mRNAs remains robust during cellular stress, early development, and cell cycle progression despite inactivation of eIF4E. Here we describe a cap-dependent pathway of translation initiation in human cells that relies on a previously unknown cap-binding activity of eIF3d, a subunit of the 800-kilodalton eIF3 complex. A 1.4 A crystal structure of the eIF3d cap-binding domain reveals unexpected homology to endonucleases involved in RNA turnover, and allows modelling of cap recognition by eIF3d. eIF3d makes specific contacts with the cap, as exemplified by cap analogue competition, and these interactions are essential for assembly of translation initiation complexes on eIF3-specialized mRNAs such as the cell proliferation regulator c-Jun (also known as JUN). The c-Jun mRNA further encodes an inhibitory RNA element that blocks eIF4E recruitment, thus enforcing alternative cap recognition by eIF3d. Our results reveal a mechanism of cap-dependent translation that is independent of eIF4E, and illustrate how modular RNA elements work together to direct specialized forms of translation initiation.
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eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation.,Lee AS, Kranzusch PJ, Doudna JA, Cate JH Nature. 2016 Aug 4;536(7614):96-9. PMID:27462815<ref>PMID:27462815</ref>
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==See Also==
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*[[Eukaryotic initiation factor 3D structures|Eukaryotic initiation factor 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5k4b" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Cate, J H.D]]
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[[Category: Large Structures]]
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[[Category: Doudna, J A]]
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[[Category: Nasonia vitripennis]]
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[[Category: Kranzusch, P J]]
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[[Category: Cate JHD]]
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[[Category: Lee, A S.Y]]
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[[Category: Doudna JA]]
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[[Category: Cap-binding domain]]
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[[Category: Kranzusch PJ]]
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[[Category: Eukaryotic translation initiation factor 3]]
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[[Category: Lee ASY]]
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[[Category: Translation]]
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Current revision

Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 1

PDB ID 5k4b

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