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1 doi: /nature11726 Supplementary Figure 1 SRP RNA constructs used in single molecule experiments. a, Secondary structure of wildtype E. coli SRP RNA, which forms an elongated hairpin structure capped by a conserved GGAA tetraloop. Pink region highlights the distal docking site for the SRP-FtsY GTPase complex observed in the crystal structure (PBD code: 2xxa, from Ataide et al, Science, 2011). b, Wildtype, 99A, and 82mer smrna constructs used in this work. c, Analytical RNA gel verified the generation and purification of smrna. smrnas (lanes 4, 6, 7) were purified from in vitro transcription mixtures (lanes 2, 5) by a preparative RNA gel, which removed the HDV ribozyme (90 nt, lane 3) and uncleaved precursor (210 ntd, lane 5). d, GTPase reactions for SRPs assembled with DNA-smRNA hybrid and with labeled FtsY. 1
2 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 2 smfret of the SRP-FtsY complex with Cy3-labeled Ffh. a, Schematics of the immobilized SRP-FtsY complex on the coverslip with Cy3-labeled Ffh. b, Fluorescent signals (upper) and FRET trajectory (lower) of the SRP-FtsY complex. Color coding is the same as in Figure 1b. The arrow denotes bleaching of Cy3. c, Zoom in of the grey box in b to show the four FRET states resolved by HMM. d, smfret histogram. e, HMM analysis of a sample FRET trajectory using different numbers of states. As the number of FRET states increases, better fits to experimental data were obtained. f, Probability score of each model in the HMM analysis in e. The probability maxed out at 4 states, which was chosen as the optimal model to describe experimental data. g, The FRET values of each state from the HMM analyses in e. Bold indicates the converged FRET values of the identified states. h, TDP of the GTPase rearrangement. i-n, Analysis of the transition kinetics between states L and H (i), L and M1 (j), L and 2 W W W. N A T U R E. C O M / N A T U R E
3 RESEARCH in the HMM analysis in e. The probability maxed out at 4 states, which was chosen as the optimal model to describe experimental data. g, The FRET values of each state from the HMM analyses in e. Bold indicates the converged FRET values of the identified states. h, TDP of the GTPase rearrangement. i-n, Analysis of the transition kinetics between states L and H (i), L and M1 (j), L and M2 (k), M1 and M2 (l), H and M1 (m), H and M2 (n). o, Summary of transition rates between different FRET states. p-r, Scatter plots of the transition dwell times of individual molecules. Each cross represents an individual molecule. 3
4 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 3 smfret analysis of the SRP-FtsY complex with labeled FtsY. a, HMM analysis of the FRET trajectory in Figure 1b using different numbers of FRET states. As the number of FRET states increases, better fits to experimental data were obtained. b, Probability score of each model in the HMM analysis in a. The probability maxed out at 4 states, which was chosen as the optimal model to describe experimental data. c, The FRET values of each state from the HMM analyses in a. Bold indicates the converged FRET values of the identified states. d-h, Analysis of the transition kinetics between states L and M1 (d), L and M2 (e), H and M1 (f), H and M2 (g), M1 and M2 (h). i-k, Scatter plots of the transition dwell times of individual molecules. Each cross represents an individual molecule. 4
5 RESEARCH Supplementary Figure 4 Activity of SRP RNA distal end mutants in GTPase reactions and in co-translational protein targeting and translocation. a, Representative data for stimulated GTPase reactions upon assembly of the SRP-FtsY complex with wildtype (red), 82mer (blue), and 99A (orange) SRP RNA. The data in the absence of SRP RNA are in black. Summary of the rate constants, with n = 5, is provided in Figure 2a. b, Schematics of the co-translational protein targeting and translocation assay. c & e, Representative data for co-translational targeting and translocation of ppl (c) and ppl signal sequence variants (e) by the wildtype and mutant SRPs. Color coding is the same as in a. Quantification of the data from three independent experiments is provided in Figures 2b and c. d, Signal sequence variants of ppl used in this study. Bold highlights the hydrophobic core of the signal sequence. 5
6 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 5 smfret data and analysis for SRP-FtsY complexes assembled with the 82mer SRP RNA. a & c, Fluorescent signals (upper) and FRET trajectory (lower) of the SRP(82mer)-FtsY complex with Cy3-labeled Ffh (a) or FtsY (c). Color coding is the same as in Figure 1b. b & d, smfret histograms of the GTPase complex with Cy3-labeled Ffh (b) or FtsY (d). 6
7 RESEARCH Supplementary Figure 6 smfret data and analyses for complexes assembled with mutant 99A RNA. a & f, Fluorescent signals (upper) and FRET trajectory (lower) of the SRP(99A)-FtsY complex with Cy3-labeled Ffh (a) or FtsY (f). Color coding is the same as in Figure 1b. b & g, smfret histograms of the GTPase complex with Cy3-labeled Ffh (b) or FtsY (g). c & h, Summary of the FRET distributions of SRP(99A)-FtsY and comparison with the wildtype complex for Cy3-labeled Ffh (c) or FtsY (h). d & i, TDP of the SRP(99A)-FtsY complex with Cy3-labeled Ffh (d) or FtsY (i). e & j, Summary of transition kinetics of the SRP(99A)- FtsY complex with Cy3-labeled Ffh (e) or FtsY (j). 7
8 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 7 smfret traces of SRP at different stages of its GTPase cycle, including free SRP (a) and the SRP- FtsY complex in the early (b) and closed (c) states. Ffh was labeled with Cy3. Color coding is the same as in Figure 1b. d, TDP of the SRP-FtsY complex in the closed state. 8
9 RESEARCH Supplementary Figure 8 Dwell time analysis of real-time GTP hydrolysis. a, Exponential fit of Δτ gave a lower limit for the GTPase rate. b, Exponential fit of the low FRET state between high FRET burst clusters. 9
10 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 9 RNC carrying a correct SRP substrate abolishes GTPase movement along the SRP RNA. a, RNCbound SRP-FtsY complex on the coverslip surface. b & f, Fluorescent signals (upper) and FRET trajectory (lower) of the SRP-FtsY complex bound to RNC FtsQ (b) or RNC luciferase (f). Color coding is the same as in Figure 1b. c-e, smfret histograms of the RNC FtsQ - SRP complex (c) and the RNC FtsQ -SRP-FtsY complex in the early (d) and closed (e) states. 10
11 RESEARCH Supplementary Figure 10 RNC s pausing effect is independent of the SRP RNA distal end. a & c, Fluorescent (upper) and FRET (lower) trajectory of the RNC FtsQ -SRP(82mer)-FtsY complex in the absence (a) and presence (c) of SecYEG. Color coding is the same as in Fig. 1b. b, smfret histogram of the RNC FtsQ -SRP(82mer)-FtsY complex. d, Representative data for GTPase assay of mutant FtsY T307A in the absence (green) and presence (grey) of RNC FtsQ. e, Summary of the k cat values from (d). Data represent mean±s.d. (n=3). 11
12 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 11 SecYEG restores GTPase movement to the SRP RNA distal site. a, SecYEG-bound RNC FtsQ -SRP- FtsY complex on the surface of the coverslip. b, smfret histogram of the RNC FtsQ -SRP-FtsY complex in the presence of 0.1% DDM. For comparison, the DDM concentration in reactions containing SecYEG is 0.07%. c, smfret histogram of the RNC FtsQ - SRP-FtsY(A335W) closed complex in the presence of SecYEG. d & e, FRET trajectory (d) and smfret histogram (e) of the SRP- FtsY complex in the presence of SecYEG but absence of RNC. Cy3-labeled Ffh was used. 12
13 RESEARCH Supplementary Figure 12 Co-localization assay of SRP and RNC. Cy3-labeled SRP (a) and Alexa647-labeled RNC FtsQ (b) colocalize before (c) and after (d) incubation with SecYEG. 13
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