SMTL ID : 8si8.1

Cryo-EM structure of TRPM7 N1098Q mutant in GDN detergent in complex with inhibitor VER155008 in closed 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: 27 residues within 4Å: Chain A: R.730, Y.922, I.969, V.973, I.992, G.993, K.994, V.996, A.997, Y.1040 Chain B: V.1009, S.1012, F.1013, P.1016, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: 3FD.3, CLR.4, POV.6, POV.7, POV.18, POV.19 Ligand excluded by PLIP POV.2: 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.7, POV.8 Ligand excluded by PLIP POV.5: 14 residues within 4Å: Chain A: H.955, V.958, A.959, L.962, I.963, L.966 Chain B: P.1067, G.1068, W.1070, L.1071 Ligands: POV.2, CLR.4, POV.7, POV.19 Ligand excluded by PLIP POV.6: 20 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 Chain B: F.1081 Chain D: W.757, L.979, N.982, Q.984 Ligands: POV.1, POV.18, POV.52 Ligand excluded by PLIP POV.7: 18 residues within 4Å: Chain A: R.728, K.916, F.919, S.920, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.1, POV.2, 3FD.3, CLR.4, POV.5 Ligand excluded by PLIP POV.8: 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.2, POV.9 Ligand excluded by PLIP POV.9: 16 residues within 4Å: Chain A: L.880, V.883, W.886, I.887, I.889, A.890, F.893, T.894, F.938, F.942, P.1130, L.1131, I.1133, L.1134 Ligands: POV.8, POV.10 Ligand excluded by PLIP POV.10: 13 residues within 4Å: Chain A: I.764, L.765, W.856, F.857, L.860, A.861, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.9, POV.11 Ligand excluded by PLIP POV.11: 18 residues within 4Å: Chain A: L.860, A.861, L.863, G.864, F.865, M.867, L.868, F.871, V.883, Q.884, I.887, Y.891, P.1130 Chain B: P.1027 Ligands: POV.10, POV.14, POV.32, DU0.33 Ligand excluded by PLIP POV.12: 5 residues within 4Å: Chain A: W.1029 Chain D: M.867 Ligands: DU0.13, POV.19, POV.65 Ligand excluded by PLIP POV.14: 24 residues within 4Å: Chain A: S.743, W.757, I.761, L.765, 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.21, POV.26, DU0.33, POV.36 Ligand excluded by PLIP POV.15: 24 residues within 4Å: Chain A: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Chain D: F.1000, A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Ligands: POV.16, POV.49, POV.55, POV.60 Ligand excluded by PLIP POV.16: 19 residues within 4Å: Chain A: C.1055, C.1065, G.1066, P.1067, W.1070, F.1074, V.1078 Chain D: L.1011, W.1029, A.1032, I.1035, V.1036 Ligands: POV.15, POV.49, POV.50, DU0.51, POV.55, CLR.58, POV.59 Ligand excluded by PLIP POV.18: 24 residues within 4Å: Chain A: F.1000, A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Chain B: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.1, POV.6, POV.19, POV.52 Ligand excluded by PLIP POV.19: 19 residues within 4Å: Chain A: L.1011, W.1029, A.1032, I.1035, V.1036 Chain B: C.1055, C.1065, G.1066, P.1067, W.1070, F.1074, V.1078 Ligands: POV.1, CLR.4, POV.5, POV.12, DU0.13, POV.18, POV.52 Ligand excluded by PLIP POV.20: 27 residues within 4Å: Chain B: R.730, Y.922, I.969, V.973, I.992, G.993, K.994, V.996, A.997, Y.1040 Chain C: V.1009, S.1012, F.1013, P.1016, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: POV.21, 3FD.23, CLR.24, POV.26, POV.27, POV.36 Ligand excluded by PLIP POV.21: 24 residues within 4Å: Chain B: F.1000, A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Chain C: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.14, POV.20, POV.26, POV.36 Ligand excluded by PLIP POV.22: 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.25, POV.27, POV.28 Ligand excluded by PLIP POV.25: 14 residues within 4Å: Chain B: H.955, V.958, A.959, L.962, I.963, L.966 Chain C: P.1067, G.1068, W.1070, L.1071 Ligands: POV.22, CLR.24, POV.27, POV.36 Ligand excluded by PLIP POV.26: 20 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 Chain C: F.1081 Ligands: POV.14, POV.20, POV.21 Ligand excluded by PLIP POV.27: 18 residues within 4Å: Chain B: R.728, K.916, F.919, S.920, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.20, POV.22, 3FD.23, CLR.24, POV.25 Ligand excluded by PLIP POV.28: 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.22, POV.29 Ligand excluded by PLIP POV.29: 16 residues within 4Å: Chain B: L.880, V.883, W.886, I.887, I.889, A.890, F.893, T.894, F.938, F.942, P.1130, L.1131, I.1133, L.1134 Ligands: POV.28, POV.30 Ligand excluded by PLIP POV.30: 13 residues within 4Å: Chain B: I.764, L.765, W.856, F.857, L.860, A.861, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.29, POV.31 Ligand excluded by PLIP POV.31: 18 residues within 4Å: Chain B: L.860, A.861, L.863, G.864, F.865, M.867, L.868, F.871, V.883, Q.884, I.887, Y.891, P.1130 Chain C: P.1027 Ligands: POV.30, POV.34, POV.35, DU0.48 Ligand excluded by PLIP POV.32: 5 residues within 4Å: Chain A: M.867 Chain B: W.1029 Ligands: POV.11, DU0.33, POV.36 Ligand excluded by PLIP POV.34: 24 residues within 4Å: Chain B: S.743, W.757, I.761, L.765, 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.31, POV.42, DU0.48, POV.53, POV.54 Ligand excluded by PLIP POV.35: 5 residues within 4Å: Chain B: M.867 Chain C: W.1029 Ligands: POV.31, DU0.48, POV.54 Ligand excluded by PLIP POV.36: 19 residues within 4Å: Chain B: L.1011, W.1029, A.1032, I.1035, V.1036 Chain C: C.1055, C.1065, G.1066, P.1067, W.1070, F.1074, V.1078 Ligands: POV.14, POV.20, POV.21, CLR.24, POV.25, POV.32, DU0.33 Ligand excluded by PLIP POV.37: 27 residues within 4Å: Chain C: R.730, Y.922, I.969, V.973, I.992, G.993, K.994, V.996, A.997, Y.1040 Chain D: V.1009, S.1012, F.1013, P.1016, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: 3FD.39, CLR.40, POV.42, POV.43, POV.53, POV.54 Ligand excluded by PLIP POV.38: 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.41, POV.43, POV.44 Ligand excluded by PLIP POV.41: 14 residues within 4Å: Chain C: H.955, V.958, A.959, L.962, I.963, L.966 Chain D: P.1067, G.1068, W.1070, L.1071 Ligands: POV.38, CLR.40, POV.43, POV.54 Ligand excluded by PLIP POV.42: 20 residues within 4Å: Chain B: W.757, 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 Chain D: F.1081 Ligands: POV.34, POV.37, POV.53 Ligand excluded by PLIP POV.43: 18 residues within 4Å: Chain C: R.728, K.916, F.919, S.920, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.37, POV.38, 3FD.39, CLR.40, POV.41 Ligand excluded by PLIP POV.44: 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.38, 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.938, F.942, P.1130, L.1131, I.1133, L.1134 Ligands: POV.44, POV.46 Ligand excluded by PLIP POV.46: 13 residues within 4Å: Chain C: I.764, L.765, W.856, F.857, L.860, A.861, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.45, POV.47 Ligand excluded by PLIP POV.47: 18 residues within 4Å: Chain C: L.860, A.861, L.863, G.864, F.865, M.867, L.868, F.871, V.883, Q.884, I.887, Y.891, P.1130 Chain D: P.1027 Ligands: POV.46, POV.49, POV.50, DU0.51 Ligand excluded by PLIP POV.49: 24 residues within 4Å: Chain C: S.743, W.757, I.761, L.765, 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.15, POV.16, POV.47, DU0.51, POV.60 Ligand excluded by PLIP POV.50: 5 residues within 4Å: Chain C: M.867 Chain D: W.1029 Ligands: POV.16, POV.47, DU0.51 Ligand excluded by PLIP POV.52: 24 residues within 4Å: Chain A: V.1004, A.1007, L.1008, L.1011 Chain D: S.743, W.757, I.761, L.765, F.855, W.856, T.859, L.860, L.863, L.975, F.978, L.979, V.981, N.982, Q.983 Ligands: POV.6, DU0.13, POV.18, POV.19, POV.65 Ligand excluded by PLIP POV.53: 24 residues within 4Å: Chain C: F.1000, A.1007, L.1010, L.1011, W.1029, S.1030, A.1032, K.1033, V.1036, F.1037, Y.1040, W.1041 Chain D: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.34, POV.37, POV.42, POV.54 Ligand excluded by PLIP POV.54: 19 residues within 4Å: Chain C: L.1011, W.1029, A.1032, I.1035, V.1036 Chain D: C.1055, C.1065, G.1066, P.1067, W.1070, F.1074, V.1078 Ligands: POV.34, POV.35, POV.37, CLR.40, POV.41, DU0.48, POV.53 Ligand excluded by PLIP POV.55: 28 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, I.1086 Chain D: R.730, Y.922, I.969, V.973, L.976, I.992, G.993, K.994, V.996, A.997, Y.1040 Ligands: POV.15, POV.16, 3FD.57, CLR.58, POV.60, POV.61 Ligand excluded by PLIP POV.56: 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.59, POV.61, POV.62 Ligand excluded by PLIP POV.59: 14 residues within 4Å: Chain A: P.1067, G.1068, W.1070, L.1071 Chain D: H.955, V.958, A.959, L.962, I.963, L.966 Ligands: POV.16, POV.56, CLR.58, POV.61 Ligand excluded by PLIP POV.60: 22 residues within 4Å: Chain A: F.1081, I.1085, I.1086 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 Ligands: POV.15, POV.49, POV.55 Ligand excluded by PLIP POV.61: 18 residues within 4Å: Chain D: R.728, K.916, F.919, S.920, Y.922, V.925, S.926, I.929, S.933, I.963, L.966, N.967, F.970 Ligands: POV.55, POV.56, 3FD.57, CLR.58, POV.59 Ligand excluded by PLIP POV.62: 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.56, POV.63 Ligand excluded by PLIP POV.63: 16 residues within 4Å: Chain D: L.880, V.883, W.886, I.887, I.889, A.890, F.893, T.894, F.938, F.942, P.1130, L.1131, I.1133, L.1134 Ligands: POV.62, POV.64 Ligand excluded by PLIP POV.64: 13 residues within 4Å: Chain D: I.764, L.765, W.856, F.857, L.860, A.861, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.63, POV.65 Ligand excluded by PLIP POV.65: 18 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.883, Q.884, I.887, Y.891, P.1130 Ligands: POV.12, DU0.13, POV.52, POV.64 Ligand excluded by PLIP

4 x 3FD: 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile(Non-covalent)

3FD.3: 21 residues within 4Å: Chain A: R.730, D.921, Y.922, F.923, V.973, L.976, D.977, A.980, V.981, V.989, M.990, I.992, G.993, K.994, V.1109, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.1, POV.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.922, A:F.923, A:A.980, A:V.989, A:Q.1113, A:F.1117, A:F.1117 Hydrogen bonds: A:D.921, A:Y.922, A:F.923, A:K.994, A:Q.1113 3FD.23: 21 residues within 4Å: Chain B: R.730, D.921, Y.922, F.923, V.973, L.976, D.977, A.980, V.981, V.989, M.990, I.992, G.993, K.994, V.1109, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.20, POV.27 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.922, B:F.923, B:A.980, B:V.989, B:Q.1113, B:F.1117 Hydrogen bonds: B:D.921, B:Y.922, B:F.923, B:K.994, B:W.1110, B:Q.1113 3FD.39: 21 residues within 4Å: Chain C: R.730, D.921, Y.922, F.923, V.973, L.976, D.977, A.980, V.981, V.989, M.990, I.992, G.993, K.994, V.1109, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.37, POV.43 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.922, C:F.923, C:A.980, C:V.989, C:Q.1113, C:F.1117, C:F.1117 Hydrogen bonds: C:D.921, C:Y.922, C:F.923, C:K.994, C:Q.1113 3FD.57: 21 residues within 4Å: Chain D: R.730, D.921, Y.922, F.923, V.973, L.976, D.977, A.980, V.981, V.989, M.990, I.992, G.993, K.994, V.1109, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.55, POV.61 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.922, D:F.923, D:A.980, D:V.989, D:Q.1113, D:F.1117, D:F.1117 Hydrogen bonds: D:Y.922, D:F.923, D:K.994, D:Q.1113

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.7, POV.19 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.1070, B:W.1070, B:L.1071, B:F.1074, B:L.1075, A:I.969, A:F.970, A:F.970, A:F.970 Hydrogen bonds: A:Y.922 CLR.24: 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.20, POV.25, POV.27, POV.36 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:W.1070, C:W.1070, C:L.1071, C:F.1074, C:L.1075, B:I.969, B:F.970, B:F.970, B:F.970 Hydrogen bonds: B:Y.922 CLR.40: 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.37, POV.41, POV.43, POV.54 10 PLIP interactions: 5 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 CLR.58: 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.16, POV.55, POV.59, POV.61 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:W.1070, A:W.1070, A:L.1071, A:F.1074, A:L.1075, D:I.969, D:F.970, D:F.970, D:F.970 Hydrogen bonds: D:Y.922

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, 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.12, POV.19, POV.52, POV.65 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.863, D:M.867, D:T.870, D:F.871, D:Y.972, A:W.1029, A:A.1032, A:I.1035 DU0.33: 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.11, POV.14, POV.32, POV.36 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.863, A:M.867, A:T.870, A:F.871, A:Y.972, B:W.1029, B:A.1032, B:I.1035 DU0.48: 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.31, POV.34, POV.35, POV.54 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.863, B:M.867, B:T.870, B:F.871, B:Y.972, C:W.1029, C:A.1032, C:I.1035 DU0.51: 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.47, POV.49, POV.50 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.863, C:M.867, C:T.870, C:F.871, C:Y.972, D:W.1029, D:I.1035

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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