SMTL ID : 8si4.1

Cryo-EM structure of TRPM7 N1098Q mutant in GDN detergent in open state

Coordinates

PDB Format Compare

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: 31 residues within 4Å: Chain A: Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, N.998, M.999, V.1003, Y.1040, Q.1113 Chain B: V.1009, S.1012, F.1013, P.1016, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082 Ligands: CLR.4, POV.5, POV.6, POV.18 Ligand excluded by PLIP POV.2: 9 residues within 4Å: Chain A: K.916, F.919, S.920, V.925, T.928, I.929, I.932 Ligands: POV.3, POV.6 Ligand excluded by PLIP POV.3: 15 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.2, POV.6, POV.7, POV.19 Ligand excluded by PLIP POV.5: 20 residues within 4Å: Chain A: V.996, A.997, N.998, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Chain B: F.1074, A.1077, V.1078 Chain D: Q.984 Ligands: POV.1, CLR.4, POV.6, POV.18, POV.19, POV.20, POV.50 Ligand excluded by PLIP POV.6: 19 residues within 4Å: Chain A: F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970, A.997 Ligands: POV.1, POV.2, POV.3, CLR.4, POV.5, POV.19 Ligand excluded by PLIP POV.7: 24 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, N.954, V.956 Ligands: POV.3, POV.8 Ligand excluded by PLIP POV.8: 16 residues within 4Å: Chain A: L.880, 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.7, POV.9 Ligand excluded by PLIP POV.9: 19 residues within 4Å: Chain A: F.857, A.861, G.864, F.865, L.868, F.871, V.875, S.882, V.883, Q.884, I.887, V.888, Y.891, P.1128, P.1130, L.1131 Chain B: P.1027 Ligands: POV.8, DU0.13 Ligand excluded by PLIP POV.10: 7 residues within 4Å: Chain A: W.1029 Chain D: M.867 Ligands: DU0.11, POV.19, POV.20, POV.50, DU0.51 Ligand excluded by PLIP POV.12: 24 residues within 4Å: Chain A: W.746, W.757, I.852, F.855, W.856, T.859, L.863, M.867, L.975, F.978, L.979, V.981, N.982, Q.983, W.1110 Chain B: F.1000, Y.1001, V.1004, A.1007, L.1008, L.1011 Ligands: POV.25, POV.30, DU0.31 Ligand excluded by PLIP POV.14: 24 residues within 4Å: Chain A: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Chain D: V.1003, M.1006, A.1007, L.1010, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041, I.1043 Ligands: POV.16, POV.55, POV.59 Ligand excluded by PLIP POV.15: 20 residues within 4Å: Chain A: G.1066, P.1067, G.1068, W.1070, L.1071 Chain D: Y.952, D.953, H.955, V.958, A.959, L.962, I.963, L.966 Ligands: POV.16, POV.56, POV.57, CLR.58, POV.59, POV.60, POV.64 Ligand excluded by PLIP POV.16: 18 residues within 4Å: Chain A: C.1055, C.1065, G.1066, T.1069, W.1070, F.1074 Chain D: L.1011, W.1029, A.1032, I.1035, V.1036 Ligands: POV.14, POV.15, POV.48, CLR.58, POV.59, POV.64, DU0.65 Ligand excluded by PLIP POV.18: 24 residues within 4Å: Chain A: V.1003, M.1006, A.1007, L.1010, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041, I.1043 Chain B: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.1, POV.5, POV.20 Ligand excluded by PLIP POV.19: 19 residues within 4Å: Chain A: Y.952, D.953, 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.5, POV.6, POV.10, POV.20 Ligand excluded by PLIP POV.20: 18 residues within 4Å: Chain A: L.1011, W.1029, A.1032, I.1035, V.1036 Chain B: C.1055, C.1065, G.1066, T.1069, W.1070, F.1074 Ligands: CLR.4, POV.5, POV.10, DU0.11, POV.18, POV.19, POV.50 Ligand excluded by PLIP POV.21: 31 residues within 4Å: Chain B: Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, N.998, M.999, V.1003, Y.1040, Q.1113 Chain C: V.1009, S.1012, F.1013, P.1016, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082 Ligands: CLR.24, POV.25, POV.26, POV.35 Ligand excluded by PLIP POV.22: 10 residues within 4Å: Chain B: K.916, F.919, S.920, V.925, T.928, I.929, I.932 Ligands: POV.23, POV.26, POV.36 Ligand excluded by PLIP POV.23: 15 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.26, POV.27, POV.36 Ligand excluded by PLIP POV.25: 20 residues within 4Å: Chain A: Q.984 Chain B: V.996, A.997, N.998, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Chain C: F.1074, A.1077, V.1078 Ligands: POV.12, POV.21, CLR.24, POV.26, POV.35, POV.36, POV.37 Ligand excluded by PLIP POV.26: 19 residues within 4Å: Chain B: F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970, A.997 Ligands: POV.21, POV.22, POV.23, CLR.24, POV.25, POV.36 Ligand excluded by PLIP POV.27: 24 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, N.954, V.956 Ligands: POV.23, POV.28 Ligand excluded by PLIP POV.28: 16 residues within 4Å: Chain B: L.880, 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.27, POV.29 Ligand excluded by PLIP POV.29: 19 residues within 4Å: Chain B: F.857, A.861, G.864, F.865, L.868, F.871, V.875, S.882, V.883, Q.884, I.887, V.888, Y.891, P.1128, P.1130, L.1131 Chain C: P.1027 Ligands: POV.28, DU0.33 Ligand excluded by PLIP POV.30: 7 residues within 4Å: Chain A: M.867 Chain B: W.1029 Ligands: POV.12, DU0.13, DU0.31, POV.36, POV.37 Ligand excluded by PLIP POV.32: 25 residues within 4Å: Chain B: W.746, W.757, I.852, F.855, W.856, T.859, L.863, M.867, L.975, F.978, L.979, V.981, N.982, Q.983, W.1110 Chain C: F.1000, Y.1001, V.1004, A.1007, L.1008, L.1011 Ligands: DU0.34, POV.42, POV.47, POV.54 Ligand excluded by PLIP POV.35: 24 residues within 4Å: Chain B: V.1003, M.1006, A.1007, L.1010, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041, I.1043 Chain C: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.21, POV.25, POV.37 Ligand excluded by PLIP POV.36: 20 residues within 4Å: Chain B: Y.952, D.953, 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.22, POV.23, CLR.24, POV.25, POV.26, POV.30, POV.37 Ligand excluded by PLIP POV.37: 17 residues within 4Å: Chain B: L.1011, W.1029, A.1032, I.1035, V.1036 Chain C: C.1055, C.1065, G.1066, T.1069, W.1070, F.1074 Ligands: CLR.24, POV.25, POV.30, DU0.31, POV.35, POV.36 Ligand excluded by PLIP POV.38: 31 residues within 4Å: Chain C: Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, N.998, M.999, V.1003, Y.1040, Q.1113 Chain D: V.1009, S.1012, F.1013, P.1016, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082 Ligands: CLR.41, POV.42, POV.43, POV.52 Ligand excluded by PLIP POV.39: 8 residues within 4Å: Chain C: F.919, S.920, V.925, T.928, I.929, I.932 Ligands: POV.40, POV.43 Ligand excluded by PLIP POV.40: 15 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.39, POV.43, POV.44, POV.53 Ligand excluded by PLIP POV.42: 20 residues within 4Å: Chain B: Q.984 Chain C: V.996, A.997, N.998, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Chain D: F.1074, A.1077, V.1078 Ligands: POV.32, POV.38, CLR.41, POV.43, POV.52, POV.53, POV.54 Ligand excluded by PLIP POV.43: 19 residues within 4Å: Chain C: F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970, A.997 Ligands: POV.38, POV.39, POV.40, CLR.41, POV.42, POV.53 Ligand excluded by PLIP POV.44: 24 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, N.954, V.956 Ligands: POV.40, POV.45 Ligand excluded by PLIP POV.45: 16 residues within 4Å: Chain C: L.880, 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.44, POV.46 Ligand excluded by PLIP POV.46: 19 residues within 4Å: Chain C: F.857, A.861, G.864, F.865, L.868, F.871, V.875, S.882, V.883, Q.884, I.887, V.888, Y.891, P.1128, P.1130, L.1131 Chain D: P.1027 Ligands: POV.45, DU0.49 Ligand excluded by PLIP POV.47: 7 residues within 4Å: Chain B: M.867 Chain C: W.1029 Ligands: POV.32, DU0.33, DU0.34, POV.53, POV.54 Ligand excluded by PLIP POV.48: 25 residues within 4Å: Chain C: W.746, W.757, I.852, F.855, W.856, T.859, L.863, M.867, L.975, F.978, L.979, V.981, N.982, Q.983, W.1110 Chain D: F.1000, Y.1001, V.1004, A.1007, L.1008, L.1011 Ligands: POV.16, POV.59, POV.64, DU0.65 Ligand excluded by PLIP POV.50: 25 residues within 4Å: Chain A: F.1000, Y.1001, V.1004, A.1007, L.1008, L.1011 Chain D: W.746, W.757, I.852, F.855, W.856, T.859, L.863, M.867, L.975, F.978, L.979, V.981, N.982, Q.983, W.1110 Ligands: POV.5, POV.10, DU0.11, POV.20 Ligand excluded by PLIP POV.52: 24 residues within 4Å: Chain C: V.1003, M.1006, A.1007, L.1010, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041, I.1043 Chain D: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.38, POV.42, POV.54 Ligand excluded by PLIP POV.53: 19 residues within 4Å: Chain C: Y.952, D.953, 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.40, CLR.41, POV.42, POV.43, POV.47, POV.54 Ligand excluded by PLIP POV.54: 18 residues within 4Å: Chain C: L.1011, W.1029, A.1032, I.1035, V.1036 Chain D: C.1055, C.1065, G.1066, T.1069, W.1070, F.1074 Ligands: POV.32, DU0.34, CLR.41, POV.42, POV.47, POV.52, POV.53 Ligand excluded by PLIP POV.55: 31 residues within 4Å: Chain A: V.1009, S.1012, F.1013, P.1016, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082 Chain D: Y.922, F.923, I.969, V.973, L.976, V.989, M.990, I.992, G.993, K.994, V.996, A.997, N.998, M.999, V.1003, Y.1040, Q.1113 Ligands: POV.14, CLR.58, POV.59, POV.60 Ligand excluded by PLIP POV.56: 10 residues within 4Å: Chain D: K.916, F.919, S.920, V.925, T.928, I.929, I.932 Ligands: POV.15, POV.57, POV.60 Ligand excluded by PLIP POV.57: 15 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.15, POV.56, POV.60, POV.61 Ligand excluded by PLIP POV.59: 21 residues within 4Å: Chain A: F.1074, A.1077, V.1078 Chain C: N.982, Q.984 Chain D: V.996, A.997, N.998, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Ligands: POV.14, POV.15, POV.16, POV.48, POV.55, CLR.58, POV.60 Ligand excluded by PLIP POV.60: 19 residues within 4Å: Chain D: F.919, S.920, D.921, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970, A.997 Ligands: POV.15, POV.55, POV.56, POV.57, CLR.58, POV.59 Ligand excluded by PLIP POV.61: 24 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, N.954, V.956 Ligands: POV.57, POV.62 Ligand excluded by PLIP POV.62: 16 residues within 4Å: Chain D: L.880, 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.61, POV.63 Ligand excluded by PLIP POV.63: 19 residues within 4Å: Chain A: P.1027 Chain D: F.857, A.861, G.864, F.865, L.868, F.871, V.875, S.882, V.883, Q.884, I.887, V.888, Y.891, P.1128, P.1130, L.1131 Ligands: DU0.51, POV.62 Ligand excluded by PLIP POV.64: 7 residues within 4Å: Chain C: M.867 Chain D: W.1029 Ligands: POV.15, POV.16, POV.48, DU0.49, DU0.65 Ligand excluded by PLIP

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 16 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.19, POV.20 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.969, A:F.970, A:F.970, A:F.970, B:W.1070, B:W.1070, B:L.1071, B:F.1074, B:L.1075 Hydrogen bonds: A:Y.922, A:S.926 Water bridges: A:S.926, A:F.970 CLR.24: 16 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.21, POV.25, POV.26, POV.36, POV.37 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.966, B:I.969, B:F.970, B:F.970, B:F.970, C:W.1070, C:W.1070, C:L.1071, C:F.1074, C:L.1075 Hydrogen bonds: B:Y.922, B:S.926 Water bridges: B:S.926, B:F.970 CLR.41: 16 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.38, POV.42, POV.43, POV.53, POV.54 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.969, C:F.970, C:F.970, C:F.970, D:W.1070, D:W.1070, D:L.1071, D:F.1074, D:L.1075 Hydrogen bonds: C:Y.922, C:S.926 Water bridges: C:S.926, C:F.970 CLR.58: 16 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.15, POV.16, POV.55, POV.59, POV.60 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:W.1070, A:W.1070, A:L.1071, A:F.1074, A:L.1075, D:L.966, D:I.969, D:F.970, D:F.970 Hydrogen bonds: D:Y.922, D:S.926 Water bridges: D:S.926, D:F.970

8 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)

DU0.11: 19 residues within 4Å: Chain A: L.1011, 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.10, POV.20, POV.50, DU0.51 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.863, D:T.870, D:F.871 DU0.13: 8 residues within 4Å: Chain A: M.867, L.868, F.871, Q.884 Chain B: P.1027 Ligands: POV.9, POV.30, DU0.31 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.867, A:L.868, A:F.871, B:P.1027 Hydrogen bonds: A:Q.884 DU0.31: 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, P.1027, S.1028, W.1029, L.1031, A.1032, I.1035 Ligands: POV.12, DU0.13, POV.30, POV.37 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.863, A:T.870, A:F.871 DU0.33: 8 residues within 4Å: Chain B: M.867, L.868, F.871, Q.884 Chain C: P.1027 Ligands: POV.29, DU0.34, POV.47 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:M.867, B:L.868, B:F.871, C:P.1027 Hydrogen bonds: B:Q.884 DU0.34: 19 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.32, DU0.33, POV.47, POV.54 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.863, B:T.870, B:F.871 DU0.49: 8 residues within 4Å: Chain C: M.867, L.868, F.871, Q.884 Chain D: P.1027 Ligands: POV.46, POV.64, DU0.65 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:M.867, C:L.868, C:F.871, D:P.1027 Hydrogen bonds: C:Q.884 DU0.51: 8 residues within 4Å: Chain A: P.1027 Chain D: M.867, L.868, F.871, Q.884 Ligands: POV.10, DU0.11, POV.63 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:M.867, D:L.868, D:F.871, A:P.1027 Hydrogen bonds: D:Q.884 DU0.65: 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, P.1027, S.1028, W.1029, L.1031, A.1032, I.1035 Ligands: POV.16, POV.48, DU0.49, POV.64 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.863, C:T.870, C:F.871

1 x CA: CALCIUM ION(Non-functional Binders)

CA.17: 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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