Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome
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1 Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome Ahmad Jomaa 1, Yu-Hsien Hwang Fu 2, Daniel Boehringer 1, Marc Leibundgut 1, Shu-ou Shan 2, and Nenad Ban 1 * 1 Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093, Switzerland 2 Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA *Correspondence to: ban@mol.biol.ethz.ch Supplementary Information:
2 Supplementary Figure 1: Assembly of the RNC-SRP-SR-Sec translocon quaternary complex. Purified components were mixed in 1:5:5:5 molar rations as described (Material and Methods) and incubated for 30 minutes at 25 C in the presence of either GMPPNP or GDP:AlFx before applying the sample on a 40% (w/v) sucrose cushion and pelleting by ultra-centrifugation. a, Pellets were resuspended in Buffer B, resolved by 12% SDS PAGE, and stained by Comassie brilliant blue. b, Supernatant fraction of lane 2 in Panel a was resolved separately by SDS PAGE as a control. In the presence of GTP analogues (GMPPNP or GDP:AlFx), we observe stoichiometric binding of all components of the quaternary complex.
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4 Supplementary Figure 2: 2D and 3D classification and refinement scheme. A total of 1,029,950 particles of the reaction containing RNC 1A9L -85, SRP, SR, and Sec translocon assembled in the presence of GDP:AlFx were semi-automatically picked with BOXER in the EMAN package. Two-dimensional classification (ML2D) was performed for 30 iterations using RELION on 4-fold binned images (80x80 pixels) with a sampling of 5.56 Å/pixel. 791,642 particles from good 2D class averages were retained and refined with an empty 70S model low-pass filtered to 60 Å resolution. Initial focused classification was performed for 30 iterations with the skip-align option and by applying a circular mask on the polypeptide exit tunnel region. Selected classes were then refined using information up to Nyquist frequency with a sampling of 1.39 Å/pixel. 121,952 particles (16%) depicted a quaternary complex with the kinked RNA structure and a density for the detergent embedded translocon, and were refined to 3.8 Å resolution. To improve the density of the translocon, an additional round of focused classification using the skipalign option was performed by applying a mask on the SRP distal region and the translocon and excluding the ribosome and the SRP M-domain regions. Further local classification was then performed using the signal subtraction approach implemented in RELION 1 by subtracting the signal of the ribosome. This was followed by a focused refinement to 4.8 Å of the particles by masking out the small ribosomal subunit. The resolution was determined based on the gold standard FSC (0.143 criterion).
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6 Supplementary Figure 3: Local resolution estimation and Fourier shell correlation plot of the cryo-em map of the quaternary complex. a, Representative cryo-em micrograph of the assembled reaction containing SRP, SR, Sec translocon and RNC assembled in the presence of GDP:AlFx. b, Corresponding Thon rings extending to 4.5 Å resolution. c, Representative 2D class averages obtained after running 30 cycles of maximum-likelihood classification. d and e, Unsharpened cryo-em map of the quaternary complex colored based on local resolution calculated using ResMap 2. The resolution extends to better than 4 Å in the core of the ribosome. The local resolution of the NG-heterodimer is ~7 Å, of the M-domain ~5 Å, and of the Sec translocon ~7-10 Å. f, Close-up view of the SRP RNA and the M-domain (SRP core) bound to the ribosome with resolved protein α helices of the M-domain and the signal sequence (SS). g, Fourier shell correlation curves for the full two half maps (black), masked half maps by masking the area of the SRP-SR-Sec translocon and excluding the ribosome (green), and map versus model (blue) are shown. Resolutions of the full map and of the map area masked around the factors were estimated according to the gold standard FSC=0.143 criterion as implemented in RELION. The resolution of the model versus map was estimated based on the FSC=0.5 criterion.
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8 Supplementary Figure 4: Conformation of the SRP RNA in the quaternary complex. a and b, Close-up views of the SRP-SR NG heterodimer in the activated state solved in the presence of the transition state analogue (GDP:AlFx; this study) and the SRP-SR in the closed state solved in the presence of the non-hydrolysable GTP analogue (GMPPNP; EMDB-8003). Atomic model of the NG-heterodimer in Panel b was generated by docking the x-ray structure of SRP-SR at the distal site (PDB:2XXA) into the EM map (EMDB-8003) and by using the M-domain as a reference (PDB: 5GAG). c, Close-up view of the GM-linker region shown at lower contour level (1.5 σ). Cryo-EM densities were filtered to 6 Å for clarity. d and e, Overlay of the atomic models in Panels a and b. Coordinates of the closed complex are colored gray. f, Sequence alignment of the NGloop depicts the sequence conservation in bacterial systems and was produced using the ClustalW WebServer 3,4.
9 Supplementary Figure 5: Secondary structure diagrams of SRP RNA from different organisms. a, Schematic and nomenclature of all SRP RNAs 5. Secondary structure of SRP RNA from a, Escherichia coli, b, Bacillus subtilis, c, Methanocaldococcus jannaschi, d, and Homo sapiens, e. RNA secondary structure diagrams were downloaded from the SRP database ( Circled regions indicate the hinge region observed in this study, also known as C- and E-loops, where the SRP RNA is kinked and untwisted, respectively.
10 Supplementary Figure 6: Orientation of the observed Sec translocon relative to the membrane. a, Cross-section of the unsharpened EM-density map of the quaternary complex showing secondary structural elements of the Sec translocon within the unstructured detergent micelle. b and c, Cut-through snapshots of the Sec translocon into the EM-density filtered to 8 Å with the homology model based on the x-ray coordinates of the isolated SecYEG (PDB:5CH4) docked as a rigid body (red). d, The proposed 20 tilt in the position of the translocon to prevent clashes with SRP and SR. The plane of the membrane is shown schematically as resolved in the structures of the native Sec translocon 6 or in nano-discs 7 bound at the ribosomal exit tunnel.
11 Supplementary Figure 7: Position of the A-domain of SR in the quaternary complex. a, Snapshot of the cryo-em density of the quaternary complex with fitted atomic coordinates. b and c, Close-up view of the circled area in Panel a, filtered to 20 Å and displayed at high and low density thresholds. Densities of the Sec translocon, SRP, and A-domain and NG-domain of SR are indicated. The surface of the ribosome is removed for clarity.
12 Supplementary Figure 8: Cryo-EM analysis of the RNC 1A9L -135 in the presence of the SRP, SR, Sec translocon and GDP:AlFx. The dataset was subjected to a similar processing approach as described in Extended Data Figure 2. Only subclasses of the focused 3D classification with recognizable features of either SRP, SR, or Sec translocon are shown. EMDB-8001 is filtered to a similar resolution as the final reconstruction for comparison.
13 DATA COLLECTION 50S-SRP-SR-SecYEG (SRP-SR-SecYEG) Final number of Particles 13,926 Pixel size (Å) 1.39 Defocus range (μm) Voltage (kv) 300 Electron does (e - Å -2 ) 20 Model Refinement Refinement Resolution (Å) 4.8 (8.4) Map Sharpening B-factor (Å 2 ) -218 Average B-factor (Å 2 ) 280 R.m.s deviations Bond length (Å) Bond angles ( o ) VALIDATION STATISTICS Validation Molprobity Score 2.35 (2.53) Clashscore, all atoms 8.37 (16.6) Good rotamers (%) 91.5 (91.3) Ramachandran Plot Favored (%) 96.8 (94.7) Allowed (%) 3.1 (4.44) Outliers(%) 0.08 (0.86) Validation (RNA) Correct sugar puckers (%) 99.5 (98.1) Good backbone conformation (%) 82.2 (71.2) Supplementary Table 1. Model and refinement statistics
14 COMPONENT CHAIN ID SOURCE COMMENT SRP RNA (distal site) 1 PDB ID 4C7O Fitted as a rigid model SRP RNA (core) 1 PDB ID 5GAG Fitted as a rigid model SRP RNA (kinked region) (res. 28:44, 70:80) 1 - Modeled Ffh (M-domain) i PDB ID 5GAG Fitted as a rigid model Ffh (NG-domain) i PDB ID 4C7O Fitted as a rigid model Ffh (GM-linker) i PDB ID 2XXA Fitted as a rigid model FtsY (NG-domain) l PDB ID 4C7O Fitted as a rigid model Signal sequence k - Modeled SecY g PDB ID 5CH4 Homology model SecE h PDB ID 5CH4 Homology model SecG j PDB ID 5CH4 Homology model 50S - PDB ID 5GAG Fitted as a rigid body Supplementary Table 2. Components of the final model used for rigid body docking and modeling
15 Region Chain ID Resolution (ResMap) SRP protein M- domain i (res ) 6.5 Signal sequence k 6.7 SRP protein NG- domain i (res ) 8.0 SRP RNA SR NG- domain l 9.2 SecYEG g,h,j 9.5 Supplementary Table 3. Local- resolution based on the atom position of the fitted model
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