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1 doi: /nature10913 Supplementary Figure 1 2F o -F c electron density maps of cognate and near-cognate trna Leu 2 in the A site of the 70S ribosome. The maps are contoured at 1.2 sigma and some of the trna domains are indicated. The A site occupancy for cognate and near-cognate trna Leu 2, as estimated from the density, is similar with a slightly more disordered variable loop and acceptor stem for the near-cognate trna Leu 2. The cognate and near-cognate trna Tyr show a similar trend (data not shown). This suggests that elbow and acceptor domains of near-cognate trnas are slightly less stabilized on the ribosome than the cognate version. In a previous study with non-cognate trna, which is efficiently rejected during decoding, we found that the elbow and acceptor domains were highly disordered reflecting that the acceptor end could not be positioned in the peptidyl transferase center on the ribosome

2 Supplementary Figure 2 The P/A-kink positions the A codon for interactions with trna. The elements involved in the kink formation are shown for the 70S ribosome with an unoccupied A site (a, PDB accession codes: 3I9B, 3I9C) and with the A site occupied by Leu cognate trna 2 (b). The main contributors to the kink stability (the P site trna, h44 of 16S rrna and magnesium ions) are illustrated. The interactions of h44 with h28 comprising the neck domain of the small subunit are depicted as well. In both panels the color codes are as follows: mrna is in yellow, the P site trna - in dark blue; h44 - in aquamarine; h28 - in cyan; magnesium - in green; H69 of 23S rrna - in grey; the 30S proteins S5 and S12 in bright green and magenta and the A site trna - in red (b). 2

3 Supplementary Figure 3 Omit averaged kick F o -F c map for the near-cognate complex with trna Leu 2 contoured at 3.5 sigma. a-c, Attempts to fit U G pair into standard Wobble conformation. d, Shows that only in a Watson-Crick conformation does the U G base pair fit the density. e, Shows that the model for the decoding center nucleotides (G530, A1492 and A1493) represents the best fit to the density and furthermore demonstrates that this area is very well defined with low flexibility and disorder. 3

4 Supplementary Figure 4 Omit averaged kick F o -F c map for the near-cognate complex with trna Tyr contoured at 3.5 sigma. a-c, Attempts to fit U G pair into standard Wobble conformation. d, Shows that only in a Watson-Crick conformation does the U G base pair fit the density. e, Shows that the model for the decoding center nucleotides (G530, A1492 and A1493) represents the best fit to the density and furthermore demonstrates that this area is very well defined with low flexibility and disorder. 4

5 Supplementary Figure 5 The G C-like G U pairs at the first and second positions of the codon-anticodon helices in the near-cognate complexes with or without paromomycin. The indicated distances (dashed lines) show that the G U pairs have a geometry very similar to a canonical Watson-Crick G C base pair (top panel). However, the data resolution does not allow us to give a definite hydrogen-bonding pattern. Interestingly, a similar situation was observed previously for a G U pair at the second position of the codonanticodon helix of a near-cognate complex in 30S crystals 32. There it was interpreted as a spatial average of the G U wobble pair in two alternative positions. See main text for a discussion of the G U mismatch at the first position in that previous study (Fig. 2c and Supplementary Fig. 6). 5

6 Supplementary Figure 6 The ribosome restrains the position of the first nucleotide of the A codon. Superposition of the trna Leu 2 anticodons from the 70S structure with a 30 nucleotide-long mrna (present study) and from the 30S structure 32 with a short mrna fragment (PDB accession code: 1N32). The comparison shows the positional shift in the first nucleotide of the A codon and the static nature of nucleotide A1493 of 16S rrna that forms part of the decoding center. ASL stands for an anticodon stem-loop. 6

7 Supplementary Figure 7 The decoding pocket around trna Leu 2 base-paired to its cognate and near-cognate codons in the absence and presence of paromomycin. a-c, Canonical codon-anticodon base-pairs at the first (a), second (b) and third (c) positions of the cognate codon-anticodon duplex. d-f, Near-cognate codon-anticodon interactions at the first (d), second (e) and third (f) positions with the first U4 G36 mismatch. g-i, Near-cognate codon-anticodon interactions at the first (g), second (h) and third (i) positions with the first U4 G36 mismatch in the presence of paromomycin; the buckling of the illustrated base-pairs 7

8 was analyzed with the 3DNA software package. For each set of panels, a schematic presentation of the codon-anticodon duplex is shown. Likely hydrogen bonds within 3Å distance are indicated by dashed lines; 2F o -F c electron density maps are contoured at 1.2 sigma. See color code in the legend to Supplementary Fig. 2. In all panels base pairs are shown in planar and perpendicular orientations. The buckling angles were measured with the 3DNA software. Due to the medium resolution of the datasets used to refine the models, the exact value of the buckling angles is not reliable. Nevertheless, there is a clear tendency towards increasing of the buckling angles from the cognate to near-cognate structures. 8

9 Supplementary Figure 8 Decoding pocket around trna Tyr base-paired to its cognate and near-cognate codons in the absence and presence of paromomycin. a-c, Canonical codon-anticodon base-pairs at the first (a), second (b) and third (c) positions of the cognate codon-anticodon duplex. d-f, Near-cognate codon-anticodon interactions at the first (d), second (e) and third (f) positions with the second G5 U35 mismatch. g-i, Near-cognate codon-anticodon interactions at the first (g), second (h) and third (i) positions with the second G5 U35 mismatch in the presence of paromomycin; the buckling of the illustrated base-pairs was analyzed with the 3DNA software package. For each set of panels, a schematic presentation of the codon-anticodon duplex is shown.. Likely hydrogen bonds within 3Å distance are indicated by dashed lines; 2F o -F c electron density maps are contoured at 1.2 sigma. See color code in the legend to Supplementary Fig. 2. See color code in the legend to Supplementary Fig. 2. Buckling angles are specified as in Supplementary Fig

10 Supplementary Figure 9 Deformation of the trna Tyr anticodon loop carrying a mismatch to the second position of the A codon. a, b, Local destabilization of the anticodon loop possibly reflected by disordering of the isopentenyl moiety of ms 2 i 6 A37 in the nearcognate state (a) versus a defined position of the modification in the cognate model (b). The 2F o -F c maps are contoured at 1.2 sigma. (c) Displacement of the 32 and 38 nucleotides which close the anticodon loop of trna. The superposition in (c) was performed using 23S rrna as reference. It has been shown earlier that the nature of nucleotides in positions 32 and 38 in trna can modulate the trna decoding capacity. For instance, mutations of A32 and U38 in trna Ala to U32 and A38 resulted in recognition of near-cognate codons by such mutated trnas 33. These data can be explained on the basis of our principle, which assumes that each particular sequence of trna anticodon loop specifies the loop deformability, thus determining whether a particular trna can be molded to fit the decoding center so that the mrna codon will be read, or if it will be rejected. 10

11 Supplementary Figure 10 Influence of the aminoglycoside paromomycin (PAR) on the decoding center. a, Differences between helices h44 and H69 in the cognate state and the near-cognate state in presence of PAR shown in green. Cognate trna Tyr is shown in red. The differences observed in the B2a bridge and H69 between the cognate state without PAR and the near-cognate state with PAR are smaller than those observed when comparing nearcognate complexes with and without PAR (see Fig. 2 in the main text). This suggests that PAR partially induces a conformation of rrna around the decoding center similar to that observed for cognate trna. b, Magnified view of changes in the A1493 phosphate position induced by PAR; color code is the same as in (a). In both panels superposition was performed using 23S rrna as reference. 11

12 Supplementary Figure 11 Tentative mechanism for propagation of the codonanticodon signal through the trna molecule. We determined that the decoding center imposes strict Watson-Crick geometrical constrains on the first and second base pairs in the codon-anticodon mini-helix. A near-cognate Watson-Crick G U pair will cost energy either due to tautomerization or due to repulsion in the base pair. Our data additionally suggest that there is a deformation of the codon-anticodon mini-helix and in the anticodon loop when a near-cognate trna carrying a G U mismatch to the first or second position enters the A site. A tautomer of G or U will have a different preferred backbone conformation of the codonanticodon mini-helix. Alternatively, repulsion would also force a G U mismatch to deviate from standard geometry. Such initial distortions of the near-cognate codon-anticodon duplex will propagate through the trna anticodon loop and the rest of the trna molecule causing it to dissociate from the ribosome. 12

13 Table S1 Data collection and refinement statistics for trna Leu 2. Leu Cognate trna 2 Leu NC trna 2 NC trna Leu 2 + PAR Data collection Space group P P P Cell dimensions a, b, c (Å) 210.2, 451.1, , 450.1, , 448.2, α, β, γ ( ) 90.0, 90.0, , 90.0, , 90.0, 90.0 Resolution (Å) ( )* ( ) ( ) R merge I/σI 12.5 (1.5)** 15.1 (1.5) 11.0 (1.4) Completeness (%) 100 (100) 99.9 (99.4) 100 (100) Redundancy 33 (33) 28 (27) 29 (27) Refinement Resolution (Å) No. reflections R work/ R free 0.20 / / / 0.24 No. atoms Protein/RNA B-factors Protein/RNA R.m.s deviations Bond lengths (Å) Bond angles (º) ML estimate of coordinate 0.85*** error (Å) PDB code (30S, 50S) 3TVF, 3TVE 3UYE, 3UYD 3UZ3,3UZ1 Respectively 5, 1, and 12 crystals were used to collect the data. *Highest resolution shell is shown in parenthesis. **I/σI = 2.0 at 3.2 Å, 3.1 Å, and 3.4 Å respectively for the three datasets. ***From Phenix. 13

14 Table S2 Data collection and refinement statistics for trna Tyr. Cognate trna Tyr NC trna Tyr NC trna Tyr + PAR Data collection Space group P P P Cell dimensions a, b, c (Å) 210.7, 451.8, , 450.9, , 450.3, α, β, γ ( ) 90.0, 90.0, , 90.0, , 90.0, 90.0 Resolution (Å) ( )* ( ) ( ) R merge I/σI 15.9 (1.4)** 8.5 (1.6) 8.3 (1.6) Completeness (%) 100 (100) 100 (100) 99.7 (99.5) Redundancy 24 (24) 20 (19) 23 (22) Refinement Resolution (Å) No. reflections R work/ R free 0.20 / / / 0.25 No. atoms Protein/RNA B-factors Protein/RNA R.m.s deviations Bond lengths (Å) Bond angles (º) ML estimate of coordinate 0.87*** error (Å) PDB code (30S, 50S) 3UZ6, 3UZ9 3UZG, 3UZF 3UZL,3UZK Respectively 2, 4, and 2 crystals were used to collect the data. *Highest resolution shell is shown in parenthesis. **I/σI = 2.0 at 3.1 Å, 3.3 Å, and 3.4 Å respectively for the three datasets. ***From Phenix. 14

15 Table S3 B-factors of the decoding center. Average B-factor Average B-factor for the decoding center* Leu Cognate trna Leu NC trna NC trna Leu 2 + PAR Cognate trna Tyr NC trna Tyr NC trna Tyr + PAR Average B-factor of the A-site codon-anticodon helix** * Elements of the decoding center. From 16S: A1492, A1493, G530. From 23S: A1913. ** The anticodon of trna in the A site (nucleotides 34-36) and the mrna codon (nucleotides 19-21). 15

16 Supplementary References 31. Jenner, L., Demeshkina, N., Yusupova, G., & Yusupov, M., Structural rearrangements of the ribosome at the trna proofreading step. Nat. Struct. Mol. Biol. 17, (2010). 32. Ogle, J.M., Murphy, F.V., Tarry, M.J., & Ramakrishnan, V., Selection of trna by the ribosome requires a transition from an open to a closed form. Cell 111, (2002). 33. Ledoux, S., Olejniczak, M., & Uhlenbeck, O.C., A sequence element that tunes Escherichia coli trna(ala)(ggc) to ensure accurate decoding. Nat. Struct. Mol. Biol. 16, (2009). 16