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5k4c

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Revision as of 10:39, 27 September 2023

Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 2

Structural highlights

5k4c is a 1 chain structure with sequence from Nasonia vitripennis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.698Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

Publication Abstract from PubMed

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.

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^[1]

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

References

↑ Lee AS, Kranzusch PJ, Doudna JA, Cate JH. eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature. 2016 Aug 4;536(7614):96-9. PMID:27462815 doi:http://dx.doi.org/10.1038/nature18954

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5k4c"

@@ Line 3: / Line 3: @@
 <StructureSection load='5k4c' size='340' side='right'caption='[[5k4c]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k4c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Nasvi Nasvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K4C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k4c]] is a 1 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=5K4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K4C FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.698&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k4b|5k4b]], [[5k4d|5k4d]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LOC100122367 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7425 NASVI])</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=5k4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4c OCA], [https://pdbe.org/5k4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k4c RCSB], [https://www.ebi.ac.uk/pdbsum/5k4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4c 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=5k4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4c OCA], [http://pdbe.org/5k4c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k4c RCSB], [http://www.ebi.ac.uk/pdbsum/5k4c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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]
+[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]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Nasvi]]
+[[Category: Nasonia vitripennis]]
-[[Category: Cate, J H.D]]
+[[Category: Cate JHD]]
-[[Category: Doudna, J A]]
+[[Category: Doudna JA]]
-[[Category: Kranzusch, P J]]
+[[Category: Kranzusch PJ]]
-[[Category: Lee, A S.Y]]
+[[Category: Lee ASY]]
-[[Category: Cap-binding domain]]
-[[Category: Eukaryotic translation initiation factor 3]]
-[[Category: Translation]]

5k4c

From Proteopedia

Revision as of 10:39, 27 September 2023

Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 2

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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