Table 2. Comparison between the binding position of ribosome-recycling factor (RRF) on the ribosome by cryo-electron microscopy (cryo-EM) and as derived from the interpretation of hydroxyl radical probing (HRP) data
|
RRF probe position, (domain) |
rRNA Target Site* |
Intensity of HRP cleavage† |
Distance (Å), this study‡ |
Distance (Å), alternative position§ |
|
E10 (I) |
H38 (A899) |
Medium |
31 |
43 |
|
|
H43 (A1067) |
Weak |
43 |
35 |
|
|
H69 (G1910) |
Weak |
20 |
28 |
|
|
H89 (C2483) |
Medium |
14 |
19 |
|
|
H90-92 (G2557) |
Weak |
25 |
17 |
|
K26 (I) |
H43 (A1067) |
Weak |
31 |
20 |
|
|
H69 (A1919) |
Weak |
36 |
42 |
|
|
h44 (A1410, A1493) |
Medium |
21, 28 |
20, 33 |
|
S56 (II) |
H43 (A1067) |
Medium |
17 |
22 |
|
|
H44 (A1095) |
Medium |
34 |
18 |
|
|
H89 (G2472) |
Weak |
24 |
24 |
|
S62 (II) |
H43 (A1067) |
Medium |
21 |
29 |
|
|
H44 (A1095) |
Medium |
29 |
38 |
|
|
H89 (G2472) |
Medium |
21 |
37 |
|
|
H90-92 (A2534, C2559) |
Medium, weak |
26, 34 |
42, 44 |
|
|
H95 (G2661) |
Strong |
20 |
38 |
|
|
h44 (A1410) |
Weak |
29 |
28 |
|
E77 (II) |
H95 (A2660) |
Medium |
45 |
20 |
|
N90 (II) |
H95 (G2661) |
Medium |
34 |
32 |
|
R154 (I) |
H74 (C2064) |
Medium |
16 |
29 |
|
|
H93 (C2601) |
Weak |
8 |
24 |
*RNA helices of the large and small ribosomal subunits are identified by "H" and "h," respectively. In brackets, we have shown the residue for each rRNA helix that were among numerous other residues identified by the HRP, and were found closest to the respective RRF probe positions by our cryo-EM study.
†
Strong, medium, and weak HRP cleavage intensities relate to the probing position within 25, 35, and 50 Å radius, respectively (1).‡
Based on the fitting shown in Fig. 3 a and b.§
Based on an alternate fit, as shown in Fig. 3c.1. Lancaster, L., Kiel, M. C., Kaji, A. & Noller, H. F. (2002) Cell 111, 129-140.