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1 doi: /nature11054 Supplementary Fig. 1 Sequence alignment of Na v Rh with NaChBac, Na v Ab, and eukaryotic Na v and Ca v homologs. Secondary structural elements of Na v Rh are indicated above the sequence alignment. Invariant amino acids are shaded in yellow. Gly208 and the corresponding residues in other homologs are shaded in red. The functionally important residues that are discussed in the manuscript are colored red. The listed channels include: Na v Rh of Rickettsiales sp. HIMB114 (also known as alpha proteobacterium HIMB114), GI: ; NaChBac of Bacillus halodurans, GI: ; Na v Ab of Arcobacter butzleri, GI: ; human Na v 1.4, GI: ; and human Ca v 1.3, GI: ;. The sequences were aligned with ClustalW. 1
2 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Fig. 2 Structural determination of Na v Rh. (a) Up to seven Hg atoms were found in each tetrameric channel. The anomalous signal for Hg was contoured at 5 σ. The refined positions of Hg atoms are represented by grey spheres. (b) A stereo view of the experimental electron density map in two perpendicular views, contoured at 3 σ. The map was calculated from experimental phases, which were derived from Hg-based, single-wavelength anomalous dispersion (SAD). 2
3 RESEARCH Supplementary Fig. 3 Representative electron density maps of Na v Rh. (a) The 2Fo-Fc electron density map for one subunit of Na v Rh, shown in cyan mesh, is contoured at 1.0 σ. (b) The 2Fo-Fc electron density for one representative slab of the pore domain, viewed from side, is contoured at 1.5 σ. (c) The 2Fo-Fc electron density for one representative slab, viewed from the periplasm and contoured at 1.5 σ, is shown in stereo views. 3
4 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Fig. 4 The structures of Na v Rh-WT and Na v Rh-G208S exhibit almost identical conformation. The stereo views of the superimposed structures are shown. 4
5 RESEARCH Supplementary Fig. 5 Structures from two crystal forms were obtained for Na v Rh. The stereo views of the crystal packing of Na v Rh in the space groups of P4 2 (a) and P (b) are shown. (c) Na v Rh structures adopt almost identical conformation in the two crystal forms. 5
6 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Fig. 6 Na v Rh exhibits an asymmetric selectivity filter. (a) The entrance to the selectivity filter is negatively charged. Shown here is the periplasmic view of the pore domain. (b) The network of intra- (left) and inter- (right) subunit hydrogen bonds stabilize the conformation of the selectivity filter of Na v Rh. Hydrogen bonds are presented as red dashes. (c)the interactions among Ser180, Ser181, and Glu183 of the selectivity filter of Na v Rh. The hydrogen-bonds are indicated by dashed lines. Note that all the side groups of Ser180 are hydrogen-bonded to the carboxylate group of Glu183 from the adjacent protomer, whereas there are different types of hydrogen bonds between Ser181 and Glu183 and between 6
7 RESEARCH Ser181 of the four subunits due to the distinct side group conformations of Ser181. Superimposition of the selectivity filter of the four Na v Rh protomers. (e) A stereo (d) presentation of the 2Fo-Fc electron density of the extracellular entrance to the selectivity filter of Na v Rh, contoured at 1.5 σ, highlights the asymmetric nature of the selectivity filter. 7
8 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Fig. 7 Characterization of the NaChBac/Na v Rh-filter chimaeric channel. (a) An alignment of the pore-forming region of the Na v Rh, NaChBac and the NaChBac/Na v Rh-filter chimaera. The selectivity filter of Na v Rh replaces that of NaChBac in the NaChBac/Na v Rh-filter chimaera (boxed; relevant residues are indicated in red letters). 8
9 RESEARCH G208S, used in crystallization of Na v Rh, corresponds to G218 in the NaChBac/Na v Rh-filter chimaera (green). (b) Example I Na traces elicited by voltage steps from a holding potential of -140 mv. The conductance-voltage relationship and the voltage dependence of inactivation were derived for NaChBac, the NaChBac/Na v Rh-filter chimaera, and the NaChBac/Na v Rh-filter chimaera with the G218S mutation. (c) Normalized conductance-voltage relationships were calculated from peak I Na elicited by 500-ms prepulse depolarizations to the indicated potentials (open circles; n <6; ± SEM). The voltage dependence of inactivation was measured as I Na reduction during a 100-ms test pulse as a function of the 500-ms prepulse potential (solid circles). (d) The potency of I Na antagonism by lidocaine or nifedipine was estimated by fitting the average percent block to the Hill Equation (see Methods). The IC 50 for nifedipine was 4 ± 2 μm for NaChBac and 2 ± 3 μm for the NaChBac/Na v Rh-filter chimaera. The estimated IC 50 for lidocaine was 123 ± 8 μm for NaChBac and 97 ± 6 μm for the NaChBac/Na v Rh-filter chimaera. n =
10 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Fig. 8 A Ca 2+ ion is bound to the inner site of the selectivity filter. (a) The omit electron density in the selectivity filter of Na v Rh, shown as magenta mesh, is contoured at 8 σ. (b) 2Fo-Fc electron density is shown in cyan mesh at 1.5 σ (upper panel) or 5 σ (lower panel) for the bound Ca 2+ ion and an associated water molecule. For visual clarity, only the pore helix bundle from two diagonal protomers are shown. 10
11 RESEARCH Supplementary Fig. 9 S3-S4 linker is flexible in the structure of Na v Rh. (a) The 2Fo-Fc electron density for the S3-S4 linkers in Mol B and Mol D, contoured at 1 σ, exhibits distinct conformations of the two regions. (b) Conformational change of S3-S4 linker in Mol B (blue) and Mol D (red) of Na v Rh as well as in Na v Ab (dark grey). (c) and (d) The S3-S4 linkers have high temperature factors in the structures of both Na v Rh and Na v Ab (PDB code: 2RVY). 11
12 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Fig. 10 Conformational change of VSDs between Na v Rh and Na v Ab. Stereo views are shown for the structural comparisons of VSDs of Na v Rh-Mol B (green) and Na v Ab (white) when superimposed relative to the S4-S5 linkers (a) or the charge transfer centers (b). 12
13 RESEARCH Legend for Movie S1 Movie S1: Structural basis for gating charge transfer. The animation illustrates the process of one charge (R4) transfer across the occluding residue Phe within the charge transfer center (CTC) on S2 segment. The morph was generated based on the structures of Na v Rh and Na v Ab with their CTCs superimposed. The protocol for the generation of this animation is described in online Methods. 13
14 RESEARCH SUPPLEMENTARY INFORMATION Table S1. Statistics of data collection and refinement of Na v Rh (G208S) Data Native (G208S) Hg-SAD (G208S) Space group P4 2 P4 2 Unit Cell (Å, ) a=163.44, c=61.07 a=164.39, c=60.89 Number of molecules in ASU 4 4 Wavelength (Å) Resolution (Å) 50~3.05 (3.16~3.05) 50~3.15 (3.26~3.15) R merge (%) 7.8 (84.5) 7.5 (88.2) I/σ 17.5 (1.6) 25.5 (2.2) Completeness (%) 99.7 (99.9) 99.5 (100.0) Number of measured reflections 120, ,974 Number of unique reflections 31,031 27,981 Redundancy 3.9 (3.9) 7.4 (7.5) Wilson B factor (Å 2 ) Refinement R-factor (%) R free (%) Number of atoms Protein main chain 3324 Protein side chain 3460 Protein all atoms 6784 Water molecules 1 Ions 2 Other entities 120 All atoms 6907 Average B value (Å 2 ) Protein main chain 94.4 Protein side chain 93.6 Protein all atoms 94.0 Water molecules 61.0 Other entities 85.4 All atoms 93.8 Rms deviations from ideal values Bonds (Å) Angle ( ) Ramachandran plot statistics (%) Most favorable 86.2 Additionally allowed 11.1 Generously allowed 2.2 Disallowed
15 RESEARCH Table S2. Statistics of data collection and refinement of Na v Rh variants Data Native (WT) Native (G208S) Space Group P4 2 P Unit Cell (Å, ) a=162.53, c=60.84 a=98.94, c= Number of molecules in ASU 4 4 Wavelength (Å) Resolution (Å) 50~3.70 (3.83~3.70) 50~4.40 (4.56~4.40) R merge (%) 7.2 (82.8) 7.6 (82.6) I/σ 17.6 (1.55) 18.2 (1.8) Completeness (%) 98.7 (98.0) 99.0 (100.0) Number of measured 66,725 51,477 reflections Number of unique reflections 17,285 12,312 Redundancy 3.9 (3.7) 4.2 (4.3) Wilson B factor (Å 2 ) R-factor (%) R free (%) Number of atoms Protein main chain Protein side chain Protein all atoms Ions 1 1 Other entities All atoms Average B value (Å 2 ) Protein main chain Protein side chain Protein all atoms Other entities All atoms Rms deviations from ideal values Bonds (Å) Angle ( ) Ramachandran plot statistics (%) Most favorable Additionally allowed Generously allowed Disallowed Values in parentheses are for the highest resolution shell. R merge =Σ h Σ i I h,i -I h /Σ h Σ i I h,i, where I h is the mean intensity of the i observations of symmetry related reflections of h. R=Σ F obs -F calc /ΣF obs, where F calc is the calculated protein structure factor from the atomic model (R free was calculated with 5% of the reflections selected). 15
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SUPPLEMENTARY INFORMATION doi:10.1038/nature11524 Supplementary discussion Functional analysis of the sugar porter family (SP) signature motifs. As seen in Fig. 5c, single point mutation of the conserved
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www.nature.com/nature 1 Figure S1 Sequence alignment. a Structure based alignment of the plgic of E. chrysanthemi (ELIC), the acetylcholine binding protein from the snail Lymnea stagnalis (AchBP, PDB code
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Table of Contents Page Supplementary Table 1. Diffraction data collection statistics 2 Supplementary Table 2. Crystallographic refinement statistics 3 Supplementary Fig. 1. casic1mfc packing in the R3
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