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1 doi:10.108/nature11899 Supplementar Table 1. Data collection and refinement statistics (+TPMP, native) (-TPMP, native) (+TPMP, recombinant) (MgCl ) (MgSO ) Data collection Space group C P 1 C P 1 1 P 1 1 Cell dimensions a, b, c (Å) 5.9, 55.7, , 78.9, , 55., , 71., , 71., ( ) 90, 119.0, 90 90, 10., 90 90, 118., 90 90, 90, 90 90, 90, 90 Resolution (Å) ( ) ( ) 50-. (.9-.0) ( ) (.5.5) R sm or R merge 0.1 (0.1) 0. (0.51) (0.611) (0.87) (0.68) I/ I 1.6 (.) 11. (6.) 1.9 (.6) 8.7 (.1).1(.8) Completeness (%) 95.1 (79.) 98.5 (99.6) 98. (95.6) 98. (99.) 99.5 (98.) Redundanc 6. (.) 1. (11.5).5 (.) 1. (1.0) 1. (6.) o. of crstals 1 Refinement Resolution (Å) ( ) ( ) (.8.0) ( ) (.51-.5) o. reflections 58,57 (,11) 7,5 (,510) 5,90 (1,67) 51,000 (,1) 5,870 (,6) R work/ R free 0.50 / 0.8 (0.95 /0.8) 0.7 / 0.1 (0.96 / 0.8) 0.70 / 0.98 (0.68 / 0.77) 0.1 / 0.7 (0.86 / 0.0) 0. / 0.71 (0.78 / 0.85) o. atoms 15,818 15,6 7,8 7,78 7,811 Protein 15,61 15,8 7,689 7,67 7,67 Ligand/ion Water B-factors Protein Ligand/ion Water R.m.s deviations Bond lengths (Å) Bond angles (º) *Highest resolution shell is shown in parenthesis. 1
2 TP MPPCP TP - lf E1~P Ca DP DP E1P[Ca ] Ca Ca Mg Ca + nh Mg + nh TG Pi EPi SO Pi MgF ~P - lf P - BeF (TG) Figure S1. Simplified reaction scheme of SERC1a. Onl forward direction is shown. TP can bind to SERC1a at various steps and ma have a regulator role. The reaction intermediates for which crstal structures obtained in this stud are shaded, and those obtained previousl are boed. Substrate analogues used for crstallisation are also shown (in italics).
3 a L6/7 P L6/7 P 0 0 M7 M7 b Y87 F56 Y87 F56 F8 I765 TG F8 TG I765 M7 V769 V6 M7 V769 V6 M88 M88 I67 I67 V77 V77 Figure S. Superimposition of atomic models of SERC1a in with and without thapsigargin (TG). a, whole molecule; b, details around the thapsigargin binding site. Yellow, without TG; green, with bound TG. The molecule shown here is that of SO. ote that the binding cavit for TG, which is lined b the, and M7 helices, is slightl narrower but empt. Differences in side chain conformation are also small. The P-domain in SO is identical to (TG) and differs from the bent configuration in MgF (ref 15).
4 E519 L56 E519 L56 K9 C561 K9 C561 SO R560 SO R560 R D67 SO R D67 SO T65 MgF K5 T5 D51 T65 MgF K5 T5 D P P Figure S. Electron densit map showing positions of sulphate ions in the SO crstal structure. The map is calculated using Fobs - Fobs (diffraction amplitudes from crstals prepared with MgSO minus those with MgCl ) and contoured at 5 σ. The atomic models for SO and that of MgF in MgF (ref. 15) are superimposed. One SO is stabilised b the Thr5 hdrol and the Gl66 amide, and the other stabilised b sn68 and rg678. Despite the high concentration of Mg (0 mm), no Mg was located in the P-domain. The atomic models for SO and MgF are aligned with the P- domain segment that contains sp51.
5 a TPMP TPMP MC MC 0 0 M6 M6 b TPMP TPMP MC MC Figure S. Superimposition of atomic models of SERC1a in with and without TPMP. Stereo pictures of the C -traces of the atomic models (ellow, +TPMP; blue gre, -TPMP) viewed in the same orientations as in Fig. 1. TPMP is shown in space fill. RMSD between the two models is 0. Å with the -domain ecluded, or 0.7 Å with the -domain included. 5
6 a b c Z Y X E5 E E E5 D59 E E51 W50 F9 Mg E09 E109 D W50 F9 W50 E11 E109 1 F9 Figure S5. large open mouth in leading to the transmembrane Ca binding sites. Water accessible surface coloured according to the surface potential. tomic models for (a), (b) and (c) are aligned with the M7-0 helices and viewed from the same direction. Transmembrane helices -M are numbered, and several marker residues are identified. Green horiontal lines show the approimate position of the ctoplasmic surface of the membrane. M6L 101 M8 T799 D E908 E771 Mg S Figure S6. Electron densit maps around the transmembrane Mg -binding site. -weighted F obs - F calc map contoured at 1 (blue net) calculated at.0 Å resolution with CS. Superimposed is an F obs - F calc map contoured at.5 (red net) calculated before introducing Mg (green sphere) and two water molecules (red spheres) into the atomic model. Viewed in the same direction as in Fig. b. 6
7 a b c 5 5 Y76 Y76 5 Y W79 W79 W79 SL W107 W107 W107 Figure S7. Electron densit maps around the groove surrounded b the, M6 and helices. The -weighted F obs - F calc maps contoured at 1. a, (native TPase, prepared from SR); b, (recombinant, devoid of SL); c,. Viewed from the ctoplasmic side. T18 L16 I0 L96 I SL W V89 L5 R7 Figure S8. composite omit electron densit map around SL and the heli. Calculated at.0 Å resolution with CS and contoured at
8 W107C/L10C V89C/V6C V89C/R7C I956C/V6C V89C/V6C (bbbr) -Xlink (KDa) (TG) -Xlink (TG) -Xlink (TG) -Xlink (TG) -Xlink (TG) * Figure S9. Cross-linking between Cs-substituted residues of SERC1a and FL- SL as detected with an anti-flg antibod. Cross-linkers used were copper phenanthroline (ecept for the rightmost panel) and dibromobimeine (bbbr; V89C/V6C). The arrowhead indicates the position of SERC1a and the asterisk SL monomer. ote that cross-linking of Leu10Cs (SL) and Trp107Cs () with bbbr becomes weaker in the order of > >. 8
9 ph 6.0 ph 7.0 ph 7.5 -bbbr (-Mg ) (TG) E1 (-Mg ) (TG) E1 (-Mg ) (TG) (kda) * * Figure S10. Effects of ph and Mg on the cross-links between Cs-substituted mutants of SERC1a and FL-SL or PL. Immunoblots probed with a monoclonal antibod against the FLG epitope attached to SL (upper panel) or with the D1 antibod (bcam) against PL (lower panel). The mutants used were: upper panel, SERC1a (V89C) and FL-SL (V6C); lower panel, SERC1a (V89C) and PL (V9C). The cross-linker used was bbbr. In -Mg, mm Mg and 5 mm EDT were included instead of 5 mm Mg. The arrowheads indicate the positions of SERC1a and the asterisk FL-SL (upper panel) or PL (lower panel) monomer. The number at the top of each lane represents the relative amount (in percentage) of cross-linked SERC-SL or SERC-PL normalised against that in at ph 7 after subtracting the one in the absence of the cross-linker (-bbbr). ote that is the preferred state for binding of both PL and SL. 9
10 (kda) * Figure S11. Sarcolipin in native sarcoplasmic reticulum membrane and affinit purified Ca -TPase preparation used for crstallisation. Left, Coomassie stained gel; right, immunoblots probed with anti-sl polclonal antibod. Lanes 1 and :.5 µg and 5 µg of rabbit sarcoplasmic reticulum membrane; lanes and :.5 µg and 5 µg of affinit purified Ca -TPase; lane 5: 0.6 µg of SL prepared from rabbit back muscle. The arrowhead indicates the position of SERC1a and the asterisk SL monomer. Densitometr of Coomassie stained gel bands shows that the content of SL relative to that of SERC1a in the purified specimen is ~0% of the original SR. 10
11 a MC MC 0 0 M6 M6 b MC MC Figure S1. Superimposition of the native and recombinant SERC1a in showing the strctural changes due to SL. The atomic model of native TPase (ellow, with bound SL) and that of recombinant TPase (blue gre, devoid of SL) were aligned with the M7-0 transmembrane helices. The small green sphere represents bound Mg. 11
12 a P M D51 D T171 E18 b F1 W9 T5 L8 V15 SL L10 V1 W107 F809 W79 11 E7 I10 M8 M6 T805 E908 D E90 L98 M7 E K97 05 M S7 V00 V6 L61 Figure S1. Strucutral changes caused b SL binding to SERC1a in. Superimpositions of the atomic model of native TPase (blue gre) with bound SL (ellow) and that of recombinant TPase (orange) devoid of SL. a, the - and P-domains aligned with the P-domain; b, the transmembrane region aligned with the M7-0 helices. The large green arrow in a indicates the rotation accompaning the transition (rotation 1 in Figs. 1 and ); small green arrows in a and b indicate the movements induced b SL binding. D51 (a, circled) is the phosphorlation residue. The small green sphere represents bound Mg and dotted lines likel hdrogen bonds in b. The binding of SL twists the heli, which in turn moves the and M helices. These changes in the transmembrane helices cause a small rearrnagement in the ctoplasmic domains. s a result, a larger rotation is required for the -domain in the transition. 1
13 a b Y9 R110 W107 SL T5 L8 F1 V15 L9 L96 V19 L97 W L99 9 W9 R110 T5 W SL V15 L8 F1 L9 V19 L96 L97 V950 W9 L99 9 Y1 c d e Y1 W107 W9 W107 W9 W9 W Figure S1. Binding mode of SL to SERC1a in. SL is shown in stick (a) or b van der Waals surface (b). SERC1a appears as blue gre surface, on which the atomic model ( and onl) is superimposed. The colour of the van der Waals surface of SL represents surface potential. ote that van der Waals contacts are not etensive on the side due to the presence of Trp residues near the ctoplasmic end of (Trp9) and lumenal end of SL (Trp). Thr5 of SL, the potential phosphorlation site, makes a tight contact with Trp9 on. The binding cleft for SL in different states are also shown (c, ; d, ; e, ). See Supplementar Movie for an animation. 1
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