SMTL ID : 8si6.1

Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in complex with agonist naltriben in closed state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

52 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 33 residues within 4Å: Chain A: S.920, Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, Y.1040, Q.1113 Chain B: V.1009, S.1012, F.1013, P.1016, F.1074, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: POV.2, CLR.4, POV.6, POV.7, POV.8, ZY8.14 Ligand excluded by PLIP POV.2: 22 residues within 4Å: Chain A: A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Chain B: C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.1, POV.6, POV.7, POV.50 Ligand excluded by PLIP POV.3: 14 residues within 4Å: Chain A: I.929, I.932, S.933, V.936, L.940, D.953, N.954, H.955, V.956, A.959, I.963 Ligands: POV.5, POV.8, POV.9 Ligand excluded by PLIP POV.5: 15 residues within 4Å: Chain A: H.955, V.958, A.959, L.962, I.963, L.966 Chain B: G.1066, P.1067, G.1068, W.1070, L.1071 Ligands: POV.3, CLR.4, POV.6, POV.8 Ligand excluded by PLIP POV.6: 17 residues within 4Å: Chain A: L.1011, W.1029, A.1032, I.1035, V.1036 Chain B: C.1055, C.1065, G.1066, W.1070, F.1074 Ligands: POV.1, POV.2, CLR.4, POV.5, DU0.13, POV.50, POV.51 Ligand excluded by PLIP POV.7: 23 residues within 4Å: Chain A: V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, M.1006, A.1007, L.1010, Y.1040, I.1043, F.1044, Q.1083 Chain B: F.1081, I.1085 Chain D: W.757, L.979, N.982, Q.984 Ligands: POV.1, POV.2, POV.50 Ligand excluded by PLIP POV.8: 17 residues within 4Å: Chain A: K.916, F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.1, POV.3, CLR.4, POV.5 Ligand excluded by PLIP POV.9: 23 residues within 4Å: Chain A: F.893, A.896, I.897, K.899, V.900, V.903, W.918, F.919, T.928, I.931, I.932, F.935, V.936, F.938, G.939, L.940, F.942, G.943, A.944, K.945, V.956 Ligands: POV.3, POV.10 Ligand excluded by PLIP POV.10: 17 residues within 4Å: Chain A: L.880, P.881, V.883, W.886, I.887, I.889, A.890, F.893, T.894, F.935, F.938, F.942, P.1130, L.1131, I.1133 Ligands: POV.9, POV.11 Ligand excluded by PLIP POV.11: 13 residues within 4Å: Chain A: L.765, F.857, L.860, A.861, G.864, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.10, POV.12, POV.15 Ligand excluded by PLIP POV.12: 23 residues within 4Å: Chain A: L.860, A.861, L.863, G.864, F.865, M.867, L.868, F.871, V.875, K.876, M.877, E.878, S.882, V.883, Q.884, I.887, Y.891, P.1130 Chain B: P.1027 Ligands: POV.11, POV.15, POV.16, DU0.29 Ligand excluded by PLIP POV.15: 27 residues within 4Å: Chain A: W.746, M.752, W.757, I.761, L.765, I.852, F.855, W.856, T.859, L.860, L.863, L.975, F.978, L.979, V.981, N.982, Q.983 Chain B: V.1004, A.1007, L.1008, L.1011 Ligands: POV.11, POV.12, POV.16, POV.19, POV.23, POV.33 Ligand excluded by PLIP POV.16: 6 residues within 4Å: Chain A: M.867 Chain B: W.1029 Ligands: POV.12, POV.15, DU0.29, POV.33 Ligand excluded by PLIP POV.17: 17 residues within 4Å: Chain A: C.1055, C.1065, G.1066, W.1070, F.1074 Chain D: L.1011, W.1029, A.1032, I.1035, V.1036 Ligands: POV.47, POV.48, POV.53, POV.54, CLR.56, POV.57, DU0.64 Ligand excluded by PLIP POV.18: 33 residues within 4Å: Chain B: S.920, Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, Y.1040, Q.1113 Chain C: V.1009, S.1012, F.1013, P.1016, F.1074, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: POV.19, CLR.21, POV.23, POV.24, ZY8.30, POV.33 Ligand excluded by PLIP POV.19: 22 residues within 4Å: Chain B: A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Chain C: C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.15, POV.18, POV.23, POV.33 Ligand excluded by PLIP POV.20: 14 residues within 4Å: Chain B: I.929, I.932, S.933, V.936, L.940, D.953, N.954, H.955, V.956, A.959, I.963 Ligands: POV.22, POV.24, POV.25 Ligand excluded by PLIP POV.22: 15 residues within 4Å: Chain B: H.955, V.958, A.959, L.962, I.963, L.966 Chain C: G.1066, P.1067, G.1068, W.1070, L.1071 Ligands: POV.20, CLR.21, POV.24, POV.33 Ligand excluded by PLIP POV.23: 23 residues within 4Å: Chain A: W.757, L.979, N.982, Q.984 Chain B: V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, M.1006, A.1007, L.1010, Y.1040, I.1043, F.1044, Q.1083 Chain C: F.1081, I.1085 Ligands: POV.15, POV.18, POV.19 Ligand excluded by PLIP POV.24: 17 residues within 4Å: Chain B: K.916, F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.18, POV.20, CLR.21, POV.22 Ligand excluded by PLIP POV.25: 23 residues within 4Å: Chain B: F.893, A.896, I.897, K.899, V.900, V.903, W.918, F.919, T.928, I.931, I.932, F.935, V.936, F.938, G.939, L.940, F.942, G.943, A.944, K.945, V.956 Ligands: POV.20, POV.26 Ligand excluded by PLIP POV.26: 17 residues within 4Å: Chain B: L.880, P.881, V.883, W.886, I.887, I.889, A.890, F.893, T.894, F.935, F.938, F.942, P.1130, L.1131, I.1133 Ligands: POV.25, POV.27 Ligand excluded by PLIP POV.27: 13 residues within 4Å: Chain B: L.765, F.857, L.860, A.861, G.864, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.26, POV.28, POV.31 Ligand excluded by PLIP POV.28: 23 residues within 4Å: Chain B: L.860, A.861, L.863, G.864, F.865, M.867, L.868, F.871, V.875, K.876, M.877, E.878, S.882, V.883, Q.884, I.887, Y.891, P.1130 Chain C: P.1027 Ligands: POV.27, POV.31, POV.32, DU0.45 Ligand excluded by PLIP POV.31: 27 residues within 4Å: Chain B: W.746, M.752, W.757, I.761, L.765, I.852, F.855, W.856, T.859, L.860, L.863, L.975, F.978, L.979, V.981, N.982, Q.983 Chain C: V.1004, A.1007, L.1008, L.1011 Ligands: POV.27, POV.28, POV.32, POV.35, POV.39, POV.52 Ligand excluded by PLIP POV.32: 6 residues within 4Å: Chain B: M.867 Chain C: W.1029 Ligands: POV.28, POV.31, DU0.45, POV.52 Ligand excluded by PLIP POV.33: 17 residues within 4Å: Chain B: L.1011, W.1029, A.1032, I.1035, V.1036 Chain C: C.1055, C.1065, G.1066, W.1070, F.1074 Ligands: POV.15, POV.16, POV.18, POV.19, CLR.21, POV.22, DU0.29 Ligand excluded by PLIP POV.34: 32 residues within 4Å: Chain C: S.920, Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, Y.1040, Q.1113 Chain D: V.1009, S.1012, F.1013, F.1074, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: POV.35, CLR.37, POV.39, POV.40, ZY8.46, POV.52 Ligand excluded by PLIP POV.35: 22 residues within 4Å: Chain C: A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Chain D: C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.31, POV.34, POV.39, POV.52 Ligand excluded by PLIP POV.36: 14 residues within 4Å: Chain C: I.929, I.932, S.933, V.936, L.940, D.953, N.954, H.955, V.956, A.959, I.963 Ligands: POV.38, POV.40, POV.41 Ligand excluded by PLIP POV.38: 15 residues within 4Å: Chain C: H.955, V.958, A.959, L.962, I.963, L.966 Chain D: G.1066, P.1067, G.1068, W.1070, L.1071 Ligands: POV.36, CLR.37, POV.40, POV.52 Ligand excluded by PLIP POV.39: 22 residues within 4Å: Chain B: L.979, N.982, Q.984 Chain C: V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, M.1006, A.1007, L.1010, Y.1040, I.1043, F.1044, Q.1083 Chain D: F.1081, I.1085 Ligands: POV.31, POV.34, POV.35 Ligand excluded by PLIP POV.40: 17 residues within 4Å: Chain C: K.916, F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.34, POV.36, CLR.37, POV.38 Ligand excluded by PLIP POV.41: 23 residues within 4Å: Chain C: F.893, A.896, I.897, K.899, V.900, V.903, W.918, F.919, T.928, I.931, I.932, F.935, V.936, F.938, G.939, L.940, F.942, G.943, A.944, K.945, V.956 Ligands: POV.36, POV.42 Ligand excluded by PLIP POV.42: 17 residues within 4Å: Chain C: L.880, P.881, V.883, W.886, I.887, I.889, A.890, F.893, T.894, F.935, F.938, F.942, P.1130, L.1131, I.1133 Ligands: POV.41, POV.43 Ligand excluded by PLIP POV.43: 13 residues within 4Å: Chain C: L.765, F.857, L.860, A.861, G.864, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.42, POV.44, POV.47 Ligand excluded by PLIP POV.44: 23 residues within 4Å: Chain C: L.860, A.861, L.863, G.864, F.865, M.867, L.868, F.871, V.875, K.876, M.877, E.878, S.882, V.883, Q.884, I.887, Y.891, P.1130 Chain D: P.1027 Ligands: POV.43, POV.47, POV.48, DU0.64 Ligand excluded by PLIP POV.47: 27 residues within 4Å: Chain C: W.746, M.752, W.757, I.761, L.765, I.852, F.855, W.856, T.859, L.860, L.863, L.975, F.978, L.979, V.981, N.982, Q.983 Chain D: V.1004, A.1007, L.1008, L.1011 Ligands: POV.17, POV.43, POV.44, POV.48, POV.54, POV.58 Ligand excluded by PLIP POV.48: 6 residues within 4Å: Chain C: M.867 Chain D: W.1029 Ligands: POV.17, POV.44, POV.47, DU0.64 Ligand excluded by PLIP POV.50: 27 residues within 4Å: Chain A: V.1004, A.1007, L.1008, L.1011 Chain D: W.746, M.752, W.757, I.761, L.765, I.852, F.855, W.856, T.859, L.860, L.863, L.975, F.978, L.979, V.981, N.982, Q.983 Ligands: POV.2, POV.6, POV.7, POV.51, POV.62, POV.63 Ligand excluded by PLIP POV.51: 6 residues within 4Å: Chain A: W.1029 Chain D: M.867 Ligands: POV.6, DU0.13, POV.50, POV.63 Ligand excluded by PLIP POV.52: 17 residues within 4Å: Chain C: L.1011, W.1029, A.1032, I.1035, V.1036 Chain D: C.1055, C.1065, G.1066, W.1070, F.1074 Ligands: POV.31, POV.32, POV.34, POV.35, CLR.37, POV.38, DU0.45 Ligand excluded by PLIP POV.53: 33 residues within 4Å: Chain A: V.1009, S.1012, F.1013, P.1016, F.1074, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Chain D: S.920, Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, Y.1040, Q.1113 Ligands: POV.17, POV.54, CLR.56, POV.58, POV.59, ZY8.65 Ligand excluded by PLIP POV.54: 22 residues within 4Å: Chain A: C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Chain D: A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Ligands: POV.17, POV.47, POV.53, POV.58 Ligand excluded by PLIP POV.55: 14 residues within 4Å: Chain D: I.929, I.932, S.933, V.936, L.940, D.953, N.954, H.955, V.956, A.959, I.963 Ligands: POV.57, POV.59, POV.60 Ligand excluded by PLIP POV.57: 15 residues within 4Å: Chain A: G.1066, P.1067, G.1068, W.1070, L.1071 Chain D: H.955, V.958, A.959, L.962, I.963, L.966 Ligands: POV.17, POV.55, CLR.56, POV.59 Ligand excluded by PLIP POV.58: 23 residues within 4Å: Chain A: F.1081, I.1085 Chain C: W.757, L.979, N.982, Q.984 Chain D: V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, M.1006, A.1007, L.1010, Y.1040, I.1043, F.1044, Q.1083 Ligands: POV.47, POV.53, POV.54 Ligand excluded by PLIP POV.59: 17 residues within 4Å: Chain D: K.916, F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.53, POV.55, CLR.56, POV.57 Ligand excluded by PLIP POV.60: 23 residues within 4Å: Chain D: F.893, A.896, I.897, K.899, V.900, V.903, W.918, F.919, T.928, I.931, I.932, F.935, V.936, F.938, G.939, L.940, F.942, G.943, A.944, K.945, V.956 Ligands: POV.55, POV.61 Ligand excluded by PLIP POV.61: 17 residues within 4Å: Chain D: L.880, P.881, V.883, W.886, I.887, I.889, A.890, F.893, T.894, F.935, F.938, F.942, P.1130, L.1131, I.1133 Ligands: POV.60, POV.62 Ligand excluded by PLIP POV.62: 13 residues within 4Å: Chain D: L.765, F.857, L.860, A.861, G.864, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.50, POV.61, POV.63 Ligand excluded by PLIP POV.63: 23 residues within 4Å: Chain A: P.1027 Chain D: L.860, A.861, L.863, G.864, F.865, M.867, L.868, F.871, V.875, K.876, M.877, E.878, S.882, V.883, Q.884, I.887, Y.891, P.1130 Ligands: DU0.13, POV.50, POV.51, POV.62 Ligand excluded by PLIP

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 15 residues within 4Å: Chain A: Y.922, S.926, L.966, I.969, F.970, V.973 Chain B: W.1070, L.1071, F.1074, L.1075, V.1078 Ligands: POV.1, POV.5, POV.6, POV.8 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.969, A:F.970, A:F.970, B:W.1070, B:W.1070, B:L.1071 Hydrogen bonds: A:Y.922, A:S.926, A:S.926 CLR.21: 15 residues within 4Å: Chain B: Y.922, S.926, L.966, I.969, F.970, V.973 Chain C: W.1070, L.1071, F.1074, L.1075, V.1078 Ligands: POV.18, POV.22, POV.24, POV.33 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.969, B:F.970, B:F.970, C:W.1070, C:W.1070, C:L.1071, C:L.1075 Hydrogen bonds: B:Y.922, B:S.926, B:S.926 CLR.37: 15 residues within 4Å: Chain C: Y.922, S.926, L.966, I.969, F.970, V.973 Chain D: W.1070, L.1071, F.1074, L.1075, V.1078 Ligands: POV.34, POV.38, POV.40, POV.52 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:W.1070, D:W.1070, D:L.1071, D:F.1074, D:V.1078, C:I.969, C:F.970, C:F.970 Hydrogen bonds: C:Y.922, C:S.926, C:S.926 CLR.56: 15 residues within 4Å: Chain A: W.1070, L.1071, F.1074, L.1075, V.1078 Chain D: Y.922, S.926, L.966, I.969, F.970, V.973 Ligands: POV.17, POV.53, POV.57, POV.59 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:W.1070, A:W.1070, A:L.1071, A:L.1075, D:I.969, D:F.970, D:F.970 Hydrogen bonds: D:Y.922, D:S.926, D:S.926

4 x DU0: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol(Non-covalent)

DU0.13: 19 residues within 4Å: Chain A: L.1011, V.1015, P.1027, S.1028, W.1029, L.1031, A.1032, I.1035 Chain D: L.863, L.866, M.867, T.870, F.871, L.874, Y.972, L.975 Ligands: POV.6, POV.51, POV.63 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:T.870, D:F.871, D:Y.972, A:W.1029, A:A.1032, A:I.1035 Hydrogen bonds: A:W.1029 DU0.29: 19 residues within 4Å: Chain A: L.863, L.866, M.867, T.870, F.871, L.874, Y.972, L.975 Chain B: L.1011, V.1015, P.1027, S.1028, W.1029, L.1031, A.1032, I.1035 Ligands: POV.12, POV.16, POV.33 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.1029, B:A.1032, B:I.1035, A:T.870, A:F.871, A:Y.972 Hydrogen bonds: B:W.1029 DU0.45: 18 residues within 4Å: Chain B: L.863, L.866, M.867, T.870, F.871, L.874, Y.972, L.975 Chain C: L.1011, P.1027, S.1028, W.1029, L.1031, A.1032, I.1035 Ligands: POV.28, POV.32, POV.52 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:T.870, B:F.871, B:Y.972, C:W.1029, C:A.1032, C:I.1035 Hydrogen bonds: C:W.1029 DU0.64: 19 residues within 4Å: Chain C: L.863, L.866, M.867, T.870, F.871, L.874, Y.972, L.975 Chain D: L.1011, V.1015, P.1027, S.1028, W.1029, L.1031, A.1032, I.1035 Ligands: POV.17, POV.44, POV.48 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:T.870, C:F.871, C:Y.972, D:W.1029, D:A.1032, D:I.1035 Hydrogen bonds: D:W.1029

4 x ZY8: (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,9,14b-hexahydro-8aH-4,8-methanobis[1]benzofuro[3,2-e:2',3'-g]isoquinoline-1,8a-diol(Non-covalent)

ZY8.14: 16 residues within 4Å: Chain A: F.855, D.921, F.923, R.974, D.977, F.978, A.980, V.981, V.989, M.990, W.1110, Q.1113, R.1114, F.1117, Y.1121 Ligands: POV.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.855, A:F.923, A:F.978, A:A.980, A:V.989, A:F.1117, A:F.1117 Hydrogen bonds: A:D.977, A:W.1110, A:Q.1113 Salt bridges: A:D.977 ZY8.30: 16 residues within 4Å: Chain B: F.855, D.921, F.923, R.974, D.977, F.978, A.980, V.981, V.989, M.990, W.1110, Q.1113, R.1114, F.1117, Y.1121 Ligands: POV.18 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.855, B:F.923, B:F.978, B:A.980, B:V.989, B:F.1117, B:F.1117 Hydrogen bonds: B:D.977, B:W.1110, B:Q.1113 Salt bridges: B:D.977 ZY8.46: 16 residues within 4Å: Chain C: F.855, D.921, F.923, R.974, D.977, F.978, A.980, V.981, V.989, M.990, W.1110, Q.1113, R.1114, F.1117, Y.1121 Ligands: POV.34 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.855, C:F.923, C:F.978, C:A.980, C:V.989, C:F.1117, C:F.1117 Hydrogen bonds: C:D.977, C:W.1110, C:Q.1113 Salt bridges: C:D.977 ZY8.65: 16 residues within 4Å: Chain D: F.855, D.921, F.923, R.974, D.977, F.978, A.980, V.981, V.989, M.990, W.1110, Q.1113, R.1114, F.1117, Y.1121 Ligands: POV.53 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.855, D:F.923, D:F.978, D:A.980, D:V.989, D:F.1117, D:F.1117 Hydrogen bonds: D:D.977, D:W.1110, D:Q.1113 Salt bridges: D:D.977

1 x CA: CALCIUM ION(Non-covalent)

CA.49: 4 residues within 4Å: Chain A: G.1045 Chain B: G.1045 Chain C: G.1045 Chain D: G.1045 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadezhdin, K.D. et al., Structural mechanisms of TRPM7 activation and inhibition. Nat Commun (2023)

Release Date

2023-05-17

Peptides

Transient receptor potential cation channel subfamily M member 7: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily M member 7

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