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1 SUPPLEMETARY IFRMATI Supplementary information for: Structure of a β 1 -adrenergic G protein-coupled receptor Tony Warne, Maria J. Serrano-Vega, Jillian G. Baker#, Rouslan Moukhametzianov, Patricia C. Edwards, Richard enderson, Andrew G.W. Leslie, Christopher G. Tate* & Gebhard F.X. Schertler* MRC Laboratory of Molecular Biology, ills Road, Cambridge CB2 0Q, UK # Institute of Cell Signalling, Medical School, Queen s Medical Centre, University of ottingham G7 2U, UK * Joint corresponding authors s cgt@mrc-lmb.cam.ac.uk gfx@mrc-lmb.cam.ac.uk Telephone +44-(0) (0) Fax +44-(0) Supplementary Information Supplementary Figures 1-10 Supplementary Tables
2 Fig S1 adrb1_melga 1 MGDGWLPPDCGPRSGGGGATAAPTGSR adrb1_human 1 MGAGVLVLGASE------PGLSSAAPLPDGAATAARLLVPASPPASLLP 44 adrb2_human 1 MGQ PGGSAFLLAPRSAPD adrb3_human 1 MAPW------PESSLAPWPDLPTLAP * * adrb1_melga 30 -QVSAEL-LSQQWEAGMSLLMALVVLLIVAGVLVIAAIGRTQRLQTLT 77 adrb1_human 45 PASESPEPLSQQWTAGMGLLMALIVLLIVAGVLVIVAIAKTPRLQTLT 94 adrb2_human 22 -DVTQQ-RDEVWVVGMGIVMSLIVLAIVFGVLVITAIAKFERLQTVT 69 adrb3_human 24 TATSGLPGVPWEAALAGALLALAVLATVGGLLVIVAIAWTPRLQTMT * ** * **.*** **.. ****.** adrb1_melga 78 LFITSLACADLVMGLLVVPFGATLVVRGTWLWGSFLCECWTSLDVLCVTA 127 adrb1_human 95 LFIMSLASADLVMGLLVVPFGATIVVWGRWEYGSFFCELWTSVDVLCVTA 144 adrb2_human 70 YFITSLACADLVMGLAVVPFGAAILMKMWTFGFWCEFWTSIDVLCVTA 119 adrb3_human 74 VFVTSLAAADLVMGLLVVPPAATLALTGWPLGATGCELWTSVDVLCVTA 123.*. ***.******* *** *... * * ** ***.******* adrb1_melga 128 SIETLCVIAIDRYLAITSPFRYQSLMTRARAKVIICTVWAISALVSFLPI 177 adrb1_human 145 SIETLCVIALDRYLAITSPFRYQSLLTRARARGLVCTVWAISALVSFLPI 194 adrb2_human 120 SIETLCVIAVDRYFAITSPFKYQSLLTKKARVIILMVWIVSGLTSFLPI 169 adrb3_human 124 SIETLCALAVDRYLAVTPLRYGALVTKRCARTAVVLVWVVSAAVSFAPI 173 ******.*.*** *.* *.*.*.*..*.. **.* ** ** adrb1_melga 178 MMWWRDEDP-QALKCYQDPGCCDFVTRAYAIASSIISFYIPLLIMIFV 226 adrb1_human 195 LMWWRAESD-EARRCYDPKCCDFVTRAYAIASSVVSFYVPLCIMAFV 243 adrb2_human 170 QMWYRATQ-EAICYAETCCDFFTQAYAIASSIVSFYVPLVIMVFV 218 adrb3_human 174 MSQWWRVGADAEAQRCSPRCCAFASMPYVLLSSSVSFYLPLLVMLFV 223..* *.* * ** *.* *. **.***.**.* ** adrb1_melga 227 YLRVYREAKEQIRKIDRCEGRFYGSQE-----QPQ--PPPLPQQPILG- 268 adrb1_human 244 YLRVFREAQKQVKKIDSCERRFLGGPARPPSPSPSPVPAPAPPPGPPRPA 293 adrb2_human 219 YSRVFQEAKRQLQKIDKSEGRFVQ LSQVEQDGR- 253 adrb3_human 224 YARVFVVATRQLRLLRGELGRFPPEES-PPAPSRSLAPAPVGTCAPPE * **. * *... ** adrb1_melga GRASKRKTSRVMAMREKALKTLGIIMGVFTLCWLPFFLV 309 adrb1_human 294 AAAATAPLAGRAGKRRPSRLVALREQKALKTLGIIMGVFTLCWLPFFLA 343 adrb2_human TGGLRR--SSKFCLKEKALKTLGIIMGTFTLCWLPFFIV 292 adrb3_human GVPACGRRPARLLPLRERALCTLGLIMGTFTLCWLPFFLA 311 *....*..** ***.*** *********.. adrb1_melga 310 IVVFR-DLVPDWLFVFFWLGYASAFPIIYCRSPDFRKAFKRLLC 358 adrb1_human 344 VVKAFR-ELVPDRLFVFFWLGYASAFPIIYCRSPDFRKAFQRLLC 392 adrb2_human 293 IVVIQD-LIRKEVYILLWIGYVSGFPLIYCRSPDFRIAFQELLC 341 adrb3_human 312 VLRALGGPSLVPGPAFLALWLGYASAFPLIYCRSPDFRSAFRRLLC 361 *... *.... **.** ** ***.********* **. *** adrb1_melga 359 FPRKADRRLAGGQPAPLPGGFISTLGSPESPGGTWSDCGGTRGGSES 408 adrb1_human 393 CARRAARRRATGDRPR ASGCLARPGPPPS 423 adrb2_human 342 LRRSSLKAYGG YS-----SGTGEQSG adrb3_human 362 RCGRRLP PEP CAAARPALFPS 382 adrb1_melga 409 SLEERSKTSRSESKMEREKILATTRFYCTFLGGDKAVFCTVLRIVKL 458 adrb1_human 424 PGAASDDDD DDVVGATPPARLLEPWAGCGGAAADSDSSLDE 465 adrb2_human YVEQ------EKEK LLCEDLPGTEDFVGQGTVPSD 398 adrb3_human 383 GVPAARS SPAQPRLCQRLDGASWGVS 408. adrb1_melga 459 FEDATCTCPTKLKMKWRFKQQA 483 adrb1_human 466 PCRPGFASESKV 477 adrb2_human 399 IDSQGRCSTDSLL 413 adrb3_human
3 AGISTS ATAGISTS oradrenaline 2 Cyanopindolol C Adrenaline Iodocyanopindolol C I Isoproterenol Carazolol R363 ICI Salmeterol 3 C CGP20712A CF 3 Supplementary Figure 2. Structures of β receptor ligands discussed in the main text. 3
4 SUPPLEMETARY IFRMATI A [SPAP] (D units) log[adrenaline](m) basal isoprenaline 10μM propranolol 30nM propranolol 300nM propranolol 3000nM adrenaline adrenaline + propranolol 30nM adrenaline + propranolol 300nM adrenaline + propranolol 3000nM B 3 -camp accumulation (dpm) log[ligand](m) basal isoprenaline 10μM ICI Supplementary Figure 3. Basal activity and agonist-induced downstream signalling from β1ar-m23. The construct expressed in the stable C cell line used in these assays (see Supplementary Methods) contained amino acid residues 1-2 and of the turkey β1-adrenergic receptor i.e. there were truncations at the - and C-termini, but CL3 was intact. (A) The coupling of β1ar-m23 was tested by incubating C-m23-SPAP cells with the agonist adrenaline and measuring the amount of secreted alkaline phosphatase (SPAP) expressed from the camp response elements due to increased intracellular camp (filled circles, log EC50 for adrenaline was ± 0.09, 96.5 ± 2.1% maximal response to isoprenaline, n=11). Agonist binding was competed by the antagonist propranolol in increasing concentrations (open circles and triangles, log KD = ± 0.05, n=13). The Schild slope of this was 0.95 ± 0.08, n=3, indicating that the interaction of the ligands with the receptor was competitive. The EC50 value for adrenaline is -6.2 compared with -7.5 for human β1ar 16. (B) The inverse agonist ICI did not reduce the background camp level in the C-m23-SPAP cells, despite binding to C-m23-SPAP cells with a log KD values of ± 0.03, n=7. 4
5 SUPPLEMETARY IFRMATI Supplementary Figure 4. Packing arrangement of β1 receptors within the unit cell. Two closely related crystal forms of β 1 AR-m23 were observed with either centred monoclinic C2 or triclinic P1 symmetry; the packing is very similar in both space groups, with 4 molecules in the P1 unit cell (red) and 8 in the C2 cell (blue), which has one axis twice as large as the comparable axis in the P1 cell. The pairs of molecules related by noncrystallographic symmetry in C2 are slightly rotated to give the P1 form. The C2 crystals diffracted anisotropically with diffraction limits varying between 2.6 and 3.5 Å, whereas the P1 crystals showed isotropic diffraction to beyond 2.7 Å. Crystallographic dyads are indicated in dark blue and crystallographic two-fold screw axes are indicated in light blue. The view is down the crystallographic b axis of the C2 cell. The crystal packing does not correspond exactly to either a Type 1 or Type 2 crystal; both hydrophilic and hydrophobic lattice contacts (Supplementary Table 3), mediated both by amino acid residues and ordered detergent molecules, are found throughout the protein. 5
6 SUPPLEMETARY IFRMATI β 1 molecule A β 1 molecule C β 1 molecule B β 1 molecule D Supplementary Figure 5. Ribbon representation of the four molecules within one unit cell of the P1 crystal form. Each of the four molecules is coloured in rainbow representation with the -terminus in blue and C-terminus in red. ctylthioglucoside detergent molecules, which pack at the interfaces between the receptors, are shown in pink and the cyanopindolol molecules are shown as space filling models. 6
7 SUPPLEMETARY IFRMATI A Rhodopsin 1GZM B β 2 AR-T4 2R1 C β 1 AR:MolA D β 1 AR:MolB Supplementary Figure 6. B factor variation for the structures of rhodopsin, β2 and β1ar-m23 receptors. igh B factors are depicted in red and decreasing through the rainbow to the lowest B factors in blue. Two different molecules of the β1 receptor are shown, molecule A and molecule B, which show the difference in structure at their -termini. 7
8 SUPPLEMETARY IFRMATI 9 β1 MolB-MolA β1 MolB - β Distance (Å) CL1 EL1 CL2 EL2 CL3 EL3 Supplementary Figure 7. Structure differences between the β 1 and β 2 receptors and between molecules A and B of the β1 receptor. The rmsd for relative positions of Cα atoms for the comparisons between receptors were determined and plotted according to amino acid position using the program LSQMA (Kleywegt (1996) Acta Cryst. D 52, 842). Differences in the region of CL3 are truncated because these residues are missing. 8
9 SUPPLEMETARY IFRMATI A 2 EL2 water a 3 water B CYP 2 D121 water W303 6 D Supplementary Figure 8. Representative regions of 2Fo-Fc electron density in EL2 and near the ligand binding pocket. (A) Co-ordination of the a + ion in EL2 by the backbone carbonyl groups from amino acid residues Cys192, Asp195, Cys198 and two waters in molecule D. There is density for two water molecules in A and D, and for one in B and C. (B) Water molecule hydrogen bonded to Trp in 6 in molecule C; Trp is highly conserved and is thought to be important for receptor activation (Shi et al., (2002) J.Biol. Chem. 277, 40989). Another water molecule, visible in molecules A and D, maintains the structure of the kink in 6, by hydrogen bonding to the carbonyl of Cys ther waters tended to be less buried, and are not conserved between β1ar and β2ar, nor even between the different molecules of β1ar, suggesting that any water structure important for receptor activation is loosely packed rather than forming a conserved hydrogen bonding network. 9
10 SUPPLEMETARY IFRMATI CL2 3 4 Y149 Supplementary Figure 9. mit map of cytoplasmic loop 2. The 2Fo-Fc map (red mesh) of molecule B was calculated after deleting the CL2 loop (residues , blue) from the initial model and before rebuilding it into its new conformation. The map is contoured at the 1 sigma level and the coordinates of the final structure are superimposed on this density, with the backbone of helices 3 and 4 shown in green. 10
11 SUPPLEMETARY IFRMATI A β 1 receptor B β 2 receptor Supplementary Figure 10. Comparison of the extracellular surface charge of β 1 AR (A) with that in β 2 AR (B). There is slightly more negative surface charge in β 1 AR (A), compared with that in β 2 AR (B). The ligand in cyan is visible from the extracellular side. 11
12 SUPPLEMETARY IFRMATI Supplementary Table 1 Data processing and refinement statistics Space group P1 Cell dimensions a, b, c (Å) 55.5, 86.8, 95.5 α, β, γ ( o ) 67.6, 73.3, 85.8 Data Processing Resolution (Å) R merge (0.666) <I/σ(I)> (1.5) Completeness (%) (95.7) Multiplicity (1.8) Wilson B factor (Å 2 ) 40.7 Refinement Total number of reflections Total number of atoms 8976 umber of waters 31 umber of detergent molecules 14 umber of sodium ions 4 2 R work R free r.m.s. deviation bonds (Å) r.m.s. deviation angles ( o ) 1.27 Mean atomic B factor (Å 2 ) 46.3 Estimated coordinate error (Å) 0.44 Ramachandran plot allowed 99.8% most favoured 94.8% outliers 0.2% 1 Values in parentheses are for the highest resolution bin ( Å) 2 R free was calculated using a randomly selected subset of 2047 reflections (5%), R work was calculated using the remaining 95% of the data (39452 reflections). 12
13 SUPPLEMETARY IFRMATI Supplementary Table 2 Alanine scanning mutagenesis data for the region around Tyr149. Stability was assessed by heating detergent-solubilised receptor at 32 C for 30 minutes and the amount of functional receptor remaining determined by a 3 -dihydroalprenolol ligand binding assay. Control samples left on ice were used to determine the functional expression level by a ligand binding assay performed in parallel 15. Mutation Functional expression (w.t.=100) Stability (w.t.=100) T144A S145A P146A F147A R148A Y149A 68 1 Q150A S151A
14 SUPPLEMETARY IFRMATI Supplementary Table 3 Amino acid residues forming lattice contacts The following residues are involved in contacts <3.75 Å between molecules. The secondary structure element is given first, followed by the actual residues. Molecule A Molecule B Molecule C Molecule D 1 41, 42, 45, 52, 53, 56 39, 41 39, 41 41, 42, 45, 46, 49, 53, 56 CL , 100, , 104 EL1 108, , 107, 108, , 107, 108, , 109, , , 115 CL2 147, 150, 151, 153, 147, 148, 151, , 152, 154, , 150, 153, , 164, 168, , 164, 167, 168, 164, 167, 168, , 164, 168, EL2 179, 180, 181, , , 196, , 180, 181, 183, 190, 193, , 210, 214, 229, 206, , , 214, CL EL3 316, 318, , 318, , , 318,
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