PDBsum entry 1d7q

Gene regulation

PDB id: 1d7q

Contents

Protein chains

14 a.a.

143 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The eif1a solution structure reveals a large RNA-Binding surface important for scanning function.

Authors

J.L.Battiste, T.V.Pestova, C.U.Hellen, G.Wagner.

Ref.

Mol Cell, 2000, 5, 109-119. [DOI no: 10.1016/S1097-2765(00)80407-4]

PubMed id

10678173

Abstract

The translation initiation factor eIF1A is necessary for directing the 43S preinitiation complex from the 5' end of the mRNA to the initiation codon in a process termed scanning. We have determined the solution structure of human eIF1A, which reveals an oligonucleotide-binding (OB) fold and an additional domain. NMR titration experiments showed that eIF1A binds single-stranded RNA oligonucleotides in a site-specific, but non-sequence-specific manner, hinting at an mRNA interaction rather than specific rRNA or tRNA binding. The RNA binding surface extends over a large area covering the canonical OB fold binding site as well as a groove leading to the second domain. Site-directed mutations at multiple positions along the RNA-binding surface were defective in the ability to properly assemble preinitiation complexes at the AUG codon in vitro.

Figure 1.
Figure 1. Sequence Homology of eIF1A-like Proteins across All KingdomsSequence alignments adapted from the paper by [25]. Amino acids that have greater than 50% identity over 12 sequences analyzed by Kyrpides (more than shown in figure) are shaded. Identities between human and yeast are shown with black circles (65% identity). Side bars indicate sequences from eukaryotes (E), archaebacteria (A), and eubacteria (B/IF1). The secondary structure of human eIF1A (determined in this paper) over the region that has observable long-range NOEs is shown below the sequence (wavy lines indicate coils or turns; arrows indicate strands; cylinders indicate helices). The secondary structure elements are labeled β for β strand, α for α and 3[10] helices, L for loops connecting β strands or helices, N for amino-terminal strand, C for carboxy-terminal strand. Loop numbering indicates the secondary structure elements connect by the loops (adapted from [32]). For instance, L12 connects strand 1 and 2, and L3α connects strand 3 and the subsequent helix 1. Organisms are: HUMAN, Homo sapiens; YEAST, Saccharomyces cerevisiae; METJA, Methanococcus jannaschii; ARCFU, Archaeoglobus fulgidus; ECOLI, Escherichia coli; BACSU, Bacillus subtilis.

Figure 5.
Figure 5. Molecular Surfaces of eIF1A(A) Three views of the electrostatic surface of eIF1A produced with the program GRASP ([33]). Positive charge is colored blue and negative red (±40 kT). Surfaces to the right are progressively rotated 90° counterclockwise around the vertical axis of the paper. eIF1A is in a different orientation from the other figures with the far right panel looking down the axis/hole of the β barrel (approximately 90° clockwise rotation of Figure 4B around horizontal axis of paper). Secondary structure elements are labeled for orientation.(B) Surface of amino acids that have backbone amide chemical shift changes upon binding RNA are colored green (same residues as Figure 4B). Yellow surfaces are amino acids that have undetectable amide resonances due to intermediate conformational exchange in the unbound protein and are not available as probes of RNA binding. The three surfaces have the same orientation as in (A).

The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 5, 109-119) copyright 2000.

Secondary reference #1

Title

Eukaryotic ribosomes require initiation factors 1 and 1a to locate initiation codons.

Authors

T.V.Pestova, S.I.Borukhov, C.U.Hellen.

Ref.

Nature, 1998, 394, 854-859. [DOI no: 10.1038/29703]

PubMed id

9732867

Figure 1.
Figure 1 Composition and purification of proteins used in translation initiation. a,c, Overview of proteins used in reconstituting translation initiation. b,Purification scheme for eIF1 and eIF1A. SDS-PAGE gels were stained with Coomassie blue. The positions of molecular weight markers are indicated to theleft of lane 6. Subunits of eIF2, eIF3 and eIF4F are indicated to the right of lanes 1-3.

Figure 5.
Figure 5 Assembly and toeprint analysis of ribosomal complexes on EMCV and CSFV mRNAs. a, EMCV; b, CSFV. Reaction mixtures contained ATP and GMP-PNP, and translation components were added when indicated (time t, in min). Full-length cDNAs are marked E. cDNA products labelled AUG[834] and AUG[826] terminated 15-17 nucleotides (nt.) from the stated EMCV codon. The cDNA product labelled C[786] terminated at this nucleotide^4. cDNA products labelled A[250], C[334], G[345] and C[387]-A[392]terminated at these nucleotides6. The positions of some EMCV and CSFV nucleotides are indicated on the left.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd