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1 SUPPLEMENTARY INFORMATION doi: /nature11539 Supplementary Figure 1 Schematic representation of plant (A) and mammalian (B) P 2B -ATPase domain organization. Actuator (A-), nucleotide binding (N-), and phosphorylation (P-) domains as well as transmembrane helices are indicated. The regulatory/autoinhibitory regions are shown as cyan boxes with corresponding sequences used in this study. 1
2 RESEARCH SUPPLEMENTARY INFORMATION W47 Supplementary Figure 2 Typical electron density (contoured at 1.8 σ in 2Fo-Fc map) showing hydrophobic anchor residue W47 in CaMBS1. 2
3 SUPPLEMENTARY INFORMATION RESEARCH F93 I64 M146 L106 M125 V56 L33 M52 F60 W47 I137 V145 L72 M37 A129 d V56 I137 L106 I79 L72 M125 F92 Supplementary Figure 3 Detailed view of hydrophobic anchor residues W47 (A) and F60 (B) involved in CaM-binding in CaMBS1 and I79 (C) and F92 (D) in CaMBS2. CaM7 is shown as ribbon, ACA8 R-domain as cartoon with anchor residues as red sticks. Residues in CaM that are within a van-der-waals distance of the ACA8R anchor residues are shown as sticks and are as follows: F93, L106, M125, A129, I137, V145, and M146 (CaM7) to W47 (R-domain); L33, M37, M52, V56, I64, and L72 (CaM7) to F60 (Rdomain); V56 and L72 (CaM7) to I79 (R-domain); L106, M125 and I137 (CaM7) to F92 (R-domain). The remaining colour code is as in Fig. 1A. 3
4 RESEARCH SUPPLEMENTARY INFORMATION a b lgi, relative s, Å -1 c p(r) Supplementary Figure 4 r, nm Comparison between crystal and solution structure of (CaM7) 2 /ACA8R complex. (A) Ab initio shape calculation using DAMMIN 41 superimposed on crystal structure of (CaM7) 2 /ACA8R complex. The results show good agreement between crystal and solution structure. (B) Comparison between experimental small-angle X-ray scattering (SAXS) data (red) and theoretical scattering data as calculated from the crystal structure of (CaM7) 2 /ACA8R complex (2:1 stoichiometry) (green line; χ = 2.38) as well as a hypothetical 1:1 stoichiometry (blue dashed line; χ = 7.76), respectively, generated using CRYSOL 49. The results clearly confirm the presence of the 2:1 complex in solution. (C) Distance distribution plot computed from the experimental data. 4
5 SUPPLEMENTARY INFORMATION RESEARCH Supplementary Figure 5 Expression level of wild-type, deletion and point mutants of ACA8, which have been physiologically and biochemically characterized. SDS-PAGE gel stained in Coomassie brilliant blue showing similar expression levels (20 μg microsomes) of ACA8 (expected size 116 kda). 5
6 RESEARCH SUPPLEMENTARY INFORMATION a b c CamBS1 CamBS2 Supplementary Figure 6 Bioinformatic analysis of CaMBSs as identified in the structure of (CaM7) 2 /ACA8Rcomplex. (A) Conservation of the newly identified CaMBS2 in plants. (B) Conservation of both CaMBSs in other ACAs. (C) Sequence motifs of CaMBS1 ad CaMBS2, respectively, derived from plant PMCA sequences. 6
7 SUPPLEMENTARY INFORMATION RESEARCH 0.10 pump activity (a.u.) Black = wild type Blue = ΔCaMBS1 Red = ΔCaMBS1+2 Λ 10 Μ 5 Α0 10 Β0 0.1 Α1 1 Β Σ1 1 Τ Γ Σ2 2 Τ Γ2 0.1 totalcam 10 totalpump 1 minca 0.01 maxca Supplementatry Figure 7 Ca 2+ concentration (a.u.) Calculated Ca 2+ -dependent activity profiles of P 2B Ca 2+ -ATPases with two (black), one (blue) or zero (red) autoinhibitory sites that can be relieved by Ca 2+ -CaM. Activity is based on a mathematical model (see methods for details) assuming indicated reaction rates. 7
8 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 8 Structural models of ACA8 in its autoinhibited and Ca2+-CaM-activated states. (A) The model for the autoinhibited state was generated by docking the N-terminal helix as observed in the (CaM7)2/ACA8R crystal structure onto an ACA8 homology model in E2 conformation. The ACA8 N-terminal autoinhibitory region containing CaMBS1 (lightgreen) and CaMBS2 (lightblue) is shown in cartoon representation. Sequence variation is shown from cyan (variable) to burgundy (conserved). Conservation scores were calculated with Consurf 46. (B) Homology model of ACA8 in its Ca2+-CaM- activated state. Binding of two CaM7 molecules (darkgreen, darkblue) to CaMBS1 and CaMBS2 of ACA8 displaces the autoinhibitory helix from the catalytic core (shown in E1 conformation) and enables domain movement that is required for the catalytic cycle. Supplementary Figure 9 (A) Homology model of ACA8 in E2 conformation shown in surface representation. 8 W W W. N A T U R E. C O M / N A T U R E Sequence variation is shown from cyan (variable) to burgundy (conserved).
9 SUPPLEMENTARY INFORMATION RESEARCH a b E252 D303 D273 D332 conserved cleft residues involved in autoinhibition Supplementary Figure 9 (A) Homology model of ACA8 in E2 conformation shown in surface representation. Sequence variation is shown from cyan (variable) to burgundy (conserved). Conservation scores were calculated with Consurf 46. A highly conserved cleft extends vertically between A- and N-/P-domain. (B) Conserved acidic residues involved in ACA8 autoinhibition are coloured yellow. 9
10 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 10 Crystals of the (CaM7) 2 /ACA8R complex from A. thaliana. Crystals were obtained by the sitting-drop vapour diffusion method at 4 C using 1.9 M (NH 4 ) 2 SO 4, 0.1 M CAPS (ph 10.5), 0.2 M Li 2 SO 4 as precipitant and grew to max. dimensions of 0.7 x 0.35 x 0.2 mm. 10
11 SUPPLEMENTARY INFORMATION RESEARCH Supplementary Table 1: Data collection and refinement statistics. Values in parentheses are for the last resolution shell ( Å). Data collection Beamline ID23-2, ESRF Space group P Wavelength (Å) Resolution range (Å) Mosaicity 0.15 Unit cell parameters a = b = Å, c = Å α = β = γ = 90 No. of unique reflections 31,551 Completeness (%) R meas (%) 8.5 (133.3) R mrgd-f (%) 6.9 (74.9) I/σ(I) 18.3 (2.3) Wilson B-factor 37.8 Complex per ASU (Z) 1 # Matthews coefficient (Å 3 Da -1 ) 2.59 # Solvent content (%) 52.6 # Refinement Resolution (Å) Completeness (%) 100 No. reflections (work/free) /
12 RESEARCH SUPPLEMENTARY INFORMATION R work (%) 22.1 R free (%) 25.3 No. amino acid residues 343 No. atoms 2922 Protein 2738 Ca 2+ 8 H 2 O 176 Average B-factor (Å 2 ) 58.6 Protein (Å 2 ) 59.4 Ca 2+ (Å 2 ) 32.0 H 2 O (Å 2 ) 48.8 R.m.s. deviations Bond length (Å) Bond angles ( ) Ramachandran analysis Favoured (%) 97.0 Outliers (%) 0.3 R meas and R mrgd-f are quality measures of the individual intensity observations and of the reduced structure-factor amplitudes, respectively 50. R meas is defined as h [n h /(n h 1)] 1/2 i nh I h I h,i / h i nh I h,i. R mrgd-f is defined as A Ih,P A Ih,Q / 0.5 ( A Ih,P + A Ih,Q ) 50. # Following the most probable solution according to statistical sampling
13 SUPPLEMENTARY INFORMATION RESEARCH Supplementary Table 2: ITC data analysis of CaM+peptide binding studies CaMBS1 CaMBS2 ACA8N(40-126) PMCA1 PMCA2 PMCA3 PMCA4 N 0.89 ± ± ± 0.06 / ± ± ± ± 0.01 ± 0.05 K (M -1 ) 7.88E7 ± 4.51E7 1.94E6 ± 2.21E5 6.17E6 ± 3.3E6 / 1.52E8 ± 9.78E7 7.27E4 ± 5.16E3 8.12E4 ± 1.00E4 1.11E5 ± 1.62E4 1.69E5 ± 9.00E3!H (cal/mol) ± ± ± 78 / ± ± ± ± ± 238!S (cal/mol/deg) / N = number of sites K = binding constant!h = heat change!s = entropy change 13
14 RESEARCH SUPPLEMENTARY INFORMATION References for Supplementary Information 50 Diederichs, K. & Karplus, P. A. Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4, (1997). 51 Kantardjieff, K. A. & Rupp, B. Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci 12, (2003). 14
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