1. Interaction of Era with the 30S Ribosomal Subunit
Manjuli R. Sharma, Chandana Barat, Daniel N. Wilson, Timothy M. Booth, Masahito Kawazoe, Chie Hori-Takemoto, Mikako Shirouzu, Shigeyuki Yokoyama, Paola Fucini, Rajendra K. Agrawal 
Molecular Cell 
Volume 18, Issue 3, Pages (April 2005)
DOI: /j.molcel
Copyright © 2005 Elsevier Inc. Terms and Conditions

2. Figure 1 Binding of Era to the 30S Ribosomal Subunit
(A) SDS-PAGE analysis of Era binding to the 30S subunit. The 30S subunit fraction, obtained by sucrose density gradient ultracentrifugation of the 30S-Era complex, was analyzed by SDS PAGE and Coomassie blue staining. Lane 1 shows the 30S-subunit proteins, and lane 4 shows the Era protein. Lanes 2 and 3 were loaded with the 30S-Era complex obtained in the presence of 2- and 4-fold molar excess of Era, respectively. Lane 5 shows a molecular weight ladder. The Era band (molecular mass ∼34 kDa) is marked by an arrow at the left.
(B and C) 3D cryo-EM map showing the binding position of Era (red) on the 30S subunit (yellow). The Era density isolated from the 30S-Era complex is superimposed on the map of the control 30S subunit. The 30S subunit is shown in (B), an interface view, and (C), a platform-side view. Landmarks and abbreviations are as follows: h, head; b, body; p, platform; n, neck; and sp, spur.
Molecular Cell  , DOI: ( /j.molcel )
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3. Figure 2
Conformational Differences between Era bound and Unbound 30S Subunits and Effect of Era Binding on the Association with the 50S Subunit
(A) Cryo-EM maps of the control (solid yellow) and the Era bound (semitransparent blue) 30S subunits are superimposed. A section of the head and platform domains has been enlarged to highlight relative movements and direction (arrows) of the subunit’s head, platform domains, and the position of Era. The 30S subunit labels are as in Figure 1.
(B) Sucrose density gradient analysis of the effect of Era binding on the association of the two ribosomal subunits. Four subpanels of (B): (i) control without Era, showing complete incorporation of 50S subunits into the 70S ribosomes; (ii–iv) Subunit reassociation performed in the presence of 1-fold (1×), 2-fold (2×), and 5-fold (5×) molar excess, respectively, of Era over 30S subunits, showing diminished 70S peaks. Era was preincubated with 30S subunits, which were present in 2-fold excess over 50S subunits.
Molecular Cell  , DOI: ( /j.molcel )
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4. Figure 3
Comparison of the X-Ray Crystallographic Structure of Era with the Cryo-EM Density Map
(A) Stereo representation of the fitted X-ray structure (Chen et al., 1999) of E. coli Era (CTD in green and NTD in blue) into the cryo-EM density map (semitransparent red). The X-ray structure of Era is embedded within the EM density, recognizable by altered hues for the two Era domains (light green for CTD and magenta for NTD), while portions of the X-ray structure that protrude from the cryo-EM density are visible in their original (green or blue) colors. The Era EM density is shown at a threshold value lower than the value used in Figure 2.
(B) The geometric pivot points (F180 and G284) that we used to obtain the best fit are highlighted. The axes (solid red lines) and planes (dashed lines) of the rotations are indicated. Ribbons in gray show the unfitted positions of the NTD and the C-terminal α helix of the CTD. The orientation of the 30S-Era complex is depicted to the lower right. The 30S subunit labels are as in Figure 1. C and N, respectively, indicate the carboxy and amino termini of Era.
Molecular Cell  , DOI: ( /j.molcel )
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5. Figure 4
Interactions between the Helix-Turn-Helix Motif of the KH Domain of Era’s CTD and the 3′ Segment of the 16S rRNA
The amino acid residues of the KH domain (green) that make direct contact with the rRNA (purple) are shown with side chains (blue). The rRNA residues either making direct contact with or in close proximity to Era are highlighted as beads (orange). Left panel depicts the overall orientation of the 30S subunit, with the 16S rRNA 3′-minor domain (purple) highlighted. The 30S subunit labels are the same as in Figure 1.
Molecular Cell  , DOI: ( /j.molcel )
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6. Figure 5
Stereo Representations of Interactions of Era with 30S-Subunit Proteins and rRNA Segments
(A) Interactions of Era (red) with proteins S2 and S7 of the head (purple) and proteins S11 and S18 of the platform (green); and (B) interactions with the 16S rRNA helices h28 and h37 of the head (blue) and helices h23 and h26 of the platform (brown). The corresponding orientations of the 30S subunit are depicted to the left of each panel. The 30S subunit labels are the same as in Figure 1.
Molecular Cell  , DOI: ( /j.molcel )
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7. Figure 6
Comparison of the Binding Positions of Era and S1 on the 30S Subunit
Binding positions of (A) Era (red) and (B) protein S1 (blue), shown side by side, in an interface view of the 30S subunit (yellow). The S1 density was isolated by comparing the protein-only map computed for the 30S-subunit portion of the E. coli 70S ribosome containing the S1 protein with the protein-only map of the S1-depleted T. thermophilus 30S subunit (also see Sengupta et al., 2001). The 30S subunit labels are as in Figure 1.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2005 Elsevier Inc. Terms and Conditions