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1 Figure S1 Electrophysiology. a ph-activation of. Two-electrode voltage clamp recordings of Xenopus oocytes expressing in comparison to waterinjected oocytes. Currents were recorded at 40 mv. The ph of the solution is indicated. b Block of currents mediated by in response to the addition of 5 mm TBA. Currents were recorded at -20 mv. c -mediated macroscopic currents recorded by the inside-out patch clamp technique at 60 mv. The ph of the intracellular solution is indicated, the pipette solution was at ph 4.0. d Reversal potential of currents mediated by the WT protein and by the mutant E221A as measured from whole-cell currents (ph 4.0) at two different salt concentrations of the extracellular solution (high salt: 130 mm NaCl, low salt: 30 mm NaCl). 1
2 Table S1 Data collection and refinement statistics WT E221A Data collection Space group C2 C2 Cell dimensions a, b, c (Å) 178.5, 133.5, , 133.7, α, β, γ ( ) 90.0, 101.6, , 102.3, 90.0 Resolution (Å) ( ) ( ) R merge 9.2 (60.7) 13.1 (54.4) I / σi 23.1 (2.6) 16.1 (2.6) Completeness (%) 99.6 (99.9) 99.1 (99.5) Redundancy 6.3 (6.5) 6.3 (6.6) Refinement Resolution (Å) No. reflections R work / R free 23.8 / / 27.6 No. atoms Protein Ligand/ion - - Water 47 - B-factors Protein Ligand/ion - - Water R.m.s deviations - Bond lengths (Å) Bond angles ( ) Values in parentheses are for highest-resolution shell. 2
3 3
4 Figure S3 Electron density. a, Stereo view of averaged electron density superimposed on the pentamer. The map (3.3 Å resolution, contoured at 1 σ) was calculated using the native amplitudes and model phases that wereimproved by cyclic fivefold NCS averaging. The view is from within themembrane. Sections of this electron density are shown in panels b-d. b, Stereo view of electron density in the pore region. The view is as in a. c, Stereo view of electron density of the putative ligandbinding region viewed from the extracellular side. d, Stereo view of electron density at the interface between the extracellular domain and the pore. The view is as in a. 4
5 20 40 QDMVSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDR--RLAFDPVRS ---APADNAADARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPG--DKP β1 β GVRVKTYEPEA IWIPEIRFVNVENARDA-DVVDISVSPDGTVQYLERFSARVL LI---VENTQIERWINNGLWVPALEFINVVGSPDTGNK-RLMLFPDGRVIYNARFLGSFS β3 β4 β5 β SPLDFRRYPFDSQTLHIYLIV-RSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVK NDMDFRLFPFDRQQFVLELEPFSY-NNQQLRFSDIQVYTENIDNEEIDEWWIRKASTHIS β7 β8 β PAN--FALED RLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSY --DIRYD-HLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESF α1 β EANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKV SERLQTSFTLMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQA α2 α3 300 ESQPARAASITRASRIAFPVVFLLANIILAFLFFGF NG--VEDDLLIQRCRLAFPLGFLAIGCVLVIRGITL α4 Figure S4 Sequence alignment. Structure-based alignment of the plgics of G. violaceous () and E. chrysanthemi (, PDB code 2VL0). Secondary structure and numbering of are indicated below and above the sequences. Secondary structure elements contributing to the two sheets in the β-sandwich of the extracellular domain are colored in red and green respectively. α-helices of the pore domain are colored in blue. Strictly conserved residues between and are colored in blue. Residues that are not defined in the electron density are colored grey. Residues contributing to the pore lining in and are highlighted in green. 5
6 Figure S5 Superposition of and. a Stereo view of a superposition of the (green) and (orange) pentamers. The proteins are shown as Cα traces. The view is from within the membrane. b Stereo view of a superposition of the two proteins viewed from the extracellular side. c Stereo view of the pore region. The view is as in b. The helices α1, α2, α3 and the connecting loops are shown. 6
7 Figure S6 and nachr pore. a Stereo view of a Cα trace of the α2-α3 helices. The respective regions of the superimposed structures of (green) and nachr (grey, PDB code 2BG9) are shown. The front subunit is removed for clarity. The view is from within the membrane. b Pore radius in and nachr. Orientation of is shown above. Molecular boundaries (-----) and transmembrane region (.. ) are indicated. Pore radius of (green) and nachr (grey) are shown. Table S2 Data collection statistics for ion soaks Cs + Rb + Zn 2+ Data collection Space group C2 C2 C2 Cell dimensions a, b, c (Å) 176.0, 133.2, , 133.0, , 132.5, α, β, γ ( ) 90.0, 101.1, , 102.3, , 102.7, 90.0 Resolution (Å) ( ) ( ) ( ) R merge 11.5 (33.0) 12.8 (77.8) 13.0 (56.7) I / σi 8.19 (3.6) 12.3 (2.6) 15.5 (3.0) Completeness (%) 98.2 (98.0) (99.7) 99.0 (100.0) Redundancy 3.5 (3.4) 6.9 (7.0) 6.3 (6.0) Values in parentheses are for highest-resolution shell. 7
8 Figure S7 Stereo view of the pore region. Residual electron density in the aqueous channel indicates the presence of ordered solvent molecules. The view is from within the membrane. The front subunit is removed for clarity. Residues of helix α2 are shown as sticks. Cyclic averaged electron density is contoured at 1 σ and shown as blue mesh. F o -F c difference electron density is contoured at 3.5 σ and shown as green mesh. 8
9 Figure S8 E221A structure. a 2F o -F c electron density at 3.6 Å (contoured at 1 σ) is shown superimposed on the pore helices of the refined E221A mutant. b Intracellular pore entry of mutant E221A (left) and the WT structure with a changed conformation of the Glu 221 side-chain ( conf2, right). The molecular surface is shown as white mesh. c Pore radii of (green), the mutant E221A (blue) and conf2 (red). Pore radii of (orange) and nachr (grey) are shown as dashed lines for comparison. 9
10 Figure S9 Ligand-binding region. a Section of the superimposed ligand-binding region of (green) and AChBP (grey, PDB code 1UV6) shown as Cα traces. Carbamylcholine bound to the AChBP is shown as sticks (C atoms colored brown). The view is from the extracellular side. b Stereo view of residues surrounding the bound carbamylcholine. Color-coding and view are as in a. Ionic interactions in are indicated. Figure S10 Interface between extracellular domain and the pore. a Cα representation of the interface between the two domains of the (green) and (orange) subunit. The view is from within the membrane. b Stereo view of residues in the interface region. The view and color-coding is as in a. Interactions between selected residues in are indicated (---). 10
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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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Supplementary Table 1: Amplitudes of three current levels. Level 0 (pa) Level 1 (pa) Level 2 (pa) TrkA- TrkH WT 200 K 0.01 ± 0.01 9.5 ± 0.01 18.7 ± 0.03 200 Na * 0.001 ± 0.01 3.9 ± 0.01 12.5 ± 0.03 200
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doi:10.1038/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
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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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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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Supplementary Table 1: Data collection, phasing and refinement statistics ChbC/Ta 6 Br 12 Native ChbC Data collection Space group P4 3 2 1 2 P4 3 2 1 2 Cell dimensions a, c (Å) 132.75, 453.57 132.81, 452.95
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doi:10.1038/nature11085 Supplementary Tables: Supplementary Table 1. Summary of crystallographic and structure refinement data Structure BRIL-NOP receptor Data collection Number of crystals 23 Space group
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Supplementary Table S1 Kinetic Analyses of the AMSH-LP mutants AMSH-LP K M (μm) k cat x 10-3 (s -1 ) WT 71.8 ± 6.3 860 ± 65.4 T353A 76.8 ± 11.7 46.3 ± 3.7 F355A 58.9 ± 10.4 5.33 ± 0.30 proximal S358A 75.1
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Dph2 SeMet (iron-free) # Dph2 (iron-free) Dph2-[4Fe-4S] Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell dimensions a, b, c (Å) 58.26, 82.08, 160.42 58.74, 81.87, 160.01 55.70, 80.53,
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