PDBsum entry 5k4c

Translation

PDB id: 5k4c

Contents

Protein chain

366 a.a.

Ligands

GOL ×3

Waters ×385

PDB id:

5k4c

Name:

Translation

Title:

Structure of eukaryotic translation initiation factor 3 subunit d (eif3d) cap binding domain from nasonia vitripennis, crystal form 2

Structure:

Eukaryotic translation initiation factor 3 subunit d. Chain: a. Fragment: unp residues 172-537. Synonym: eif3d,eukaryotic translation initiation factor 3 subunit 7. Engineered: yes

Source:

Nasonia vitripennis. Parasitic wasp. Organism_taxid: 7425. Gene: loc100122367. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.70Å R-factor: 0.163 R-free: 0.196

Authors:

P.J.Kranzusch,A.S.Y.Lee,J.A.Doudna,J.H.D.Cate

Key ref:

A.S.Lee et al. (2016). eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature, 536, 96-99. PubMed id: 27462815 DOI: 10.1038/nature18954

Date:

20-May-16 Release date: 27-Jul-16

Protein chain

K7IM66  (EIF3D_NASVI) -  Eukaryotic translation initiation factor 3 subunit D from Nasonia vitripennis

Seq: 558 a.a.

Struc: 366 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/nature18954

Nature 536:96-99 (2016)

PubMed id: 27462815

eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation.

A.S.Lee, P.J.Kranzusch, J.A.Doudna, J.H.Cate.

ABSTRACT

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 Å 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.