Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states

Yatime et al. 10.1073/pnas.0706784104.

Supporting Information

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SI Figure 5
SI Figure 6
SI Figure 7
SI Figure 8
SI Figure 9
SI Figure 10

SI Figure 5

Fig. 5. Alignment of eukaryotic/archaeal initiation factor (e/aIF2)b sequences. Forty-three eukaryotic and 30 archaeal e/aIF2b sequences were aligned. N-terminal sequences corresponding to the eukaryote-specific domain are not represented. For the sake of clarity, only some representative sequences are shown. Conservations were scored, however, for the entire set of aligned sequences. Strictly conserved residues (no more than two exceptions of the 73 aligned sequences) are red. Positions with conservative replacements are yellow. Residues strictly conserved in either eukaryotic eIF2b or archaeal aIF2b are green. The numberings and the secondary structure elements of Sulfolobus solfataricus (Ss)-aIF2b are schematized below the sequences. Note that residues and secondary structure elements belonging to the a-, b-, and g-subunits are indicated throughout by a-, b-, and g- prefixes, respectively.

SI Figure 6

Fig. 6. Alignment of e/aIF2g sequences. Seventy-two eukaryotic and 34 archaeal e/aIF2g sequences were aligned. N-terminal extensions present in eukaryotic sequences are not represented. For the sake of clarity, only some representative sequences are shown. Residue conservations were scored, however, for the entire set of aligned sequences. Strictly conserved residues (no more than two exceptions of the 106 aligned sequences) are colored in red. Positions with conservative replacements are yellow. Residues strictly conserved either in eukaryotic eIF2g or archaeal aIF2g are green. The numbering and the secondary structure elements of Ss-aIF2g are schematized below the sequences.

SI Figure 7

Fig. 7. Positions of the switch regions. The stereoview was obtained from the superimposition of domain I of Ss-aIF2a3bg on that of Ss-aIF2a3b1g. Ss-aIF2a3bg is colored as follows: switch 1 is red, the region that links switch 1 to switch 2 is yellow, and switch 2 is orange. GDP, Pi, and the liganded water molecule are yellow. Ss-aIF2a3b1g is colored as follows: switch 1 is blue, the region that links switch 1 to switch 2 is cyan, and switch 2 is pale cyan. GDP and magnesium are blue, whereas water molecules bound to magnesium are gray.

SI Figure 8

Fig. 8. aIF2bg interfaces. (A) Ss-aIF2a3bg structure. The b-subunit is shown as a surface on which the residues strictly conserved in archaeal aIF2b are red, and the residues with conservative replacements (SI Fig. 5) are in yellow. The residues of b shown in green correspond with sites of missense mutations that lead to translation initiation at non-AUG codon in yeast (1-5). b-K118, b-K121, b-S122, b-A132, b-P135, and b-V136 correspond with R248, R253, L254, S264, S267, and V268, respectively. [For the sake of clarity, positions of the missense mutations affecting the b-a1 helix (6) are not represented.] The g subunit is shown as a yellow illustration, with the switch 1 region in red and the switch 2 region in orange. (B) Same as A, but the view is rotated by 90° around a vertical axis. (C) Pyrococcus furiosus (Pf)-aIF2bg structure (7). The b subunit is shown as a surface, with the same color coding as in A. The g subunit is shown as a pale yellow illustration, with the switch 1 region in red and the switch 2 region in orange.

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SI Figure 9

Fig. 9. Comparison of the structure of aIF2b with those of eIF5 and eIF1. (a) aIF2b of the present aIF2a3bg structure. (b) The N-terminal a-b domain of eIF5 and the zinc-binding domain of eIF5 are gray and black, respectively (1). eIF5 was superimposed to the ZBD in aIF2b (rms of 1.9 Å for 37 Ca atoms compared). (c) eIF5 was superimposed to the aIF2b central a-b domain (rms of 2.1 Å for 66 Ca atoms compared). (d) eIF1 (2) in gray was superimposed to the aIF2b central a-b domain (rms of 2.0 Å for 60 Ca atoms compared).