SMTL ID : 8si3.1

Cryo-EM structure of TRPM7 in GDN detergent in apo 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: 29 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, Y.1040 Chain B: V.1009, S.1012, F.1013, F.1074, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: POV.2, CLR.4, POV.7, POV.18 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: D.1053, C.1055, A.1056, W.1070, P.1073, F.1074, A.1077 Ligands: POV.1, POV.7, POV.18, POV.48 Ligand excluded by PLIP POV.3: 13 residues within 4Å: Chain A: I.929, I.932, S.933, V.936, L.940, K.945, N.954, H.955, V.956, A.959, I.963 Ligands: POV.6, POV.8 Ligand excluded by PLIP POV.5: 13 residues within 4Å: Chain A: S.743, W.746, M.747, D.977, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117, I.1118 Ligands: POV.14 Ligand excluded by PLIP POV.6: 16 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.18 Ligand excluded by PLIP POV.7: 16 residues within 4Å: Chain A: Y.922, V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Chain B: F.1081 Chain D: L.979, N.982, Q.984 Ligands: POV.1, POV.2, POV.48 Ligand excluded by PLIP POV.8: 20 residues within 4Å: Chain A: F.893, A.896, K.899, V.900, W.918, 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.9 Ligand excluded by PLIP POV.9: 17 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, L.1134 Ligands: POV.8, POV.10 Ligand excluded by PLIP POV.10: 13 residues within 4Å: Chain A: I.764, L.765, F.857, L.860, A.861, G.864, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.9, POV.11 Ligand excluded by PLIP POV.11: 19 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: E.1026, P.1027 Ligands: POV.10, POV.14, POV.30, DU0.31 Ligand excluded by PLIP POV.12: 6 residues within 4Å: Chain A: W.1029 Chain D: M.867 Ligands: DU0.13, POV.18, POV.48, POV.59 Ligand excluded by PLIP POV.14: 26 residues within 4Å: Chain A: 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, Q.984 Chain B: V.1004, A.1007, L.1008, L.1011 Ligands: POV.5, POV.11, POV.20, POV.25, POV.30, DU0.31, POV.33 Ligand excluded by PLIP POV.15: 22 residues within 4Å: Chain A: D.1053, C.1055, A.1056, 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.16, POV.47, POV.50, POV.55 Ligand excluded by PLIP POV.16: 18 residues within 4Å: Chain A: C.1055, C.1065, G.1066, P.1067, W.1070, F.1074 Chain D: L.1011, W.1029, A.1032, I.1035, V.1036 Ligands: POV.15, POV.47, POV.50, CLR.52, POV.54, POV.60, DU0.61 Ligand excluded by PLIP POV.18: 18 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 Ligands: POV.1, POV.2, CLR.4, POV.6, POV.12, DU0.13, POV.48 Ligand excluded by PLIP POV.19: 29 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, Y.1040 Chain C: V.1009, S.1012, F.1013, F.1074, L.1075, A.1077, V.1078, Y.1079, F.1081, V.1082, I.1086 Ligands: POV.20, CLR.22, POV.25, POV.33 Ligand excluded by PLIP POV.20: 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: D.1053, C.1055, A.1056, W.1070, P.1073, F.1074, A.1077 Ligands: POV.14, POV.19, POV.25, POV.33 Ligand excluded by PLIP POV.21: 13 residues within 4Å: Chain B: I.929, I.932, S.933, V.936, L.940, K.945, N.954, H.955, V.956, A.959, I.963 Ligands: POV.24, POV.26 Ligand excluded by PLIP POV.23: 13 residues within 4Å: Chain B: S.743, W.746, M.747, D.977, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117, I.1118 Ligands: POV.32 Ligand excluded by PLIP POV.24: 17 residues within 4Å: Chain B: Y.952, D.953, H.955, V.958, A.959, L.962, I.963, L.966, F.970 Chain C: G.1066, P.1067, G.1068, W.1070, L.1071 Ligands: POV.21, CLR.22, POV.33 Ligand excluded by PLIP POV.25: 17 residues within 4Å: Chain A: L.979, N.982, Q.984 Chain B: Y.922, V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Chain C: F.1081 Ligands: POV.14, POV.19, POV.20, CLR.22 Ligand excluded by PLIP POV.26: 20 residues within 4Å: Chain B: F.893, A.896, K.899, V.900, W.918, 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.21, POV.27 Ligand excluded by PLIP POV.27: 17 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, L.1134 Ligands: POV.26, POV.28 Ligand excluded by PLIP POV.28: 13 residues within 4Å: Chain B: I.764, L.765, F.857, L.860, A.861, G.864, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.27, POV.29 Ligand excluded by PLIP POV.29: 19 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: E.1026, P.1027 Ligands: POV.28, POV.32, POV.45, DU0.46 Ligand excluded by PLIP POV.30: 6 residues within 4Å: Chain A: M.867 Chain B: W.1029 Ligands: POV.11, POV.14, DU0.31, POV.33 Ligand excluded by PLIP POV.32: 25 residues within 4Å: Chain B: 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.23, POV.29, POV.35, POV.40, POV.45, DU0.46, POV.49 Ligand excluded by PLIP POV.33: 18 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 Ligands: POV.14, POV.19, POV.20, CLR.22, POV.24, POV.30, DU0.31 Ligand excluded by PLIP POV.34: 29 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, Y.1040 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.40, POV.49 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: D.1053, C.1055, A.1056, W.1070, P.1073, F.1074, A.1077 Ligands: POV.32, POV.34, POV.40, POV.49 Ligand excluded by PLIP POV.36: 13 residues within 4Å: Chain C: I.929, I.932, S.933, V.936, L.940, K.945, N.954, H.955, V.956, A.959, I.963 Ligands: POV.39, POV.41 Ligand excluded by PLIP POV.38: 13 residues within 4Å: Chain C: S.743, W.746, M.747, D.977, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117, I.1118 Ligands: POV.47 Ligand excluded by PLIP POV.39: 16 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.36, CLR.37, POV.49 Ligand excluded by PLIP POV.40: 17 residues within 4Å: Chain B: L.979, N.982, Q.984 Chain C: Y.922, V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Chain D: F.1081 Ligands: POV.32, POV.34, POV.35, CLR.37 Ligand excluded by PLIP POV.41: 20 residues within 4Å: Chain C: F.893, A.896, K.899, V.900, W.918, 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, 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, L.1134 Ligands: POV.41, POV.43 Ligand excluded by PLIP POV.43: 13 residues within 4Å: Chain C: I.764, 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 Ligand excluded by PLIP POV.44: 19 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: E.1026, P.1027 Ligands: POV.43, POV.47, POV.60, DU0.61 Ligand excluded by PLIP POV.45: 6 residues within 4Å: Chain B: M.867 Chain C: W.1029 Ligands: POV.29, POV.32, DU0.46, POV.49 Ligand excluded by PLIP POV.47: 25 residues within 4Å: Chain C: 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.38, POV.44, POV.55, POV.60, DU0.61 Ligand excluded by PLIP POV.48: 25 residues within 4Å: Chain A: V.1004, A.1007, L.1008, L.1011 Chain D: 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.2, POV.7, POV.12, DU0.13, POV.18, POV.53, POV.59 Ligand excluded by PLIP POV.49: 18 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 Ligands: POV.32, POV.34, POV.35, CLR.37, POV.39, POV.45, DU0.46 Ligand excluded by PLIP POV.50: 30 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: 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, Y.1040 Ligands: POV.15, POV.16, CLR.52, POV.55 Ligand excluded by PLIP POV.51: 13 residues within 4Å: Chain D: I.929, I.932, S.933, V.936, L.940, K.945, N.954, H.955, V.956, A.959, I.963 Ligands: POV.54, POV.56 Ligand excluded by PLIP POV.53: 13 residues within 4Å: Chain D: S.743, W.746, M.747, D.977, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117, I.1118 Ligands: POV.48 Ligand excluded by PLIP POV.54: 16 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.51, CLR.52 Ligand excluded by PLIP POV.55: 16 residues within 4Å: Chain A: F.1081 Chain C: L.979, N.982, Q.984 Chain D: Y.922, V.996, A.997, M.999, F.1000, Y.1001, V.1003, V.1004, A.1007 Ligands: POV.15, POV.47, POV.50 Ligand excluded by PLIP POV.56: 20 residues within 4Å: Chain D: F.893, A.896, K.899, V.900, W.918, 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.51, POV.57 Ligand excluded by PLIP POV.57: 17 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, L.1134 Ligands: POV.56, POV.58 Ligand excluded by PLIP POV.58: 13 residues within 4Å: Chain D: I.764, L.765, F.857, L.860, A.861, G.864, V.883, I.887, P.1128, P.1130, L.1131 Ligands: POV.57, POV.59 Ligand excluded by PLIP POV.59: 19 residues within 4Å: Chain A: E.1026, 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.48, POV.58 Ligand excluded by PLIP POV.60: 6 residues within 4Å: Chain C: M.867 Chain D: W.1029 Ligands: POV.16, POV.44, POV.47, DU0.61 Ligand excluded by PLIP

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 14 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.6, POV.18 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.1071, B:F.1074, B:F.1074, B:F.1074, B:L.1075, B:V.1078, A:L.966, A:I.969, A:F.970, A:F.970, A:F.970 Hydrogen bonds: A:Y.922, A:S.926, A:S.926 CLR.22: 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.19, POV.24, POV.25, POV.33 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:L.966, B:I.969, B:I.969, B:F.970, B:F.970, B:F.970, C:L.1071, C:F.1074, C:F.1074, C:F.1074, C:L.1075, C:V.1078 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.39, POV.40, POV.49 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.966, C:I.969, C:F.970, C:F.970, C:F.970, D:L.1071, D:F.1074, D:F.1074, D:F.1074, D:L.1075, D:V.1078 Hydrogen bonds: C:Y.922, C:S.926, C:S.926 CLR.52: 14 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.50, POV.54 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain D Hydrophobic interactions: A:L.1071, A:F.1074, A:F.1074, A:F.1074, A:L.1075, A:V.1078, D:L.966, D:I.969, D:I.969, D:F.970, 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, 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.18, POV.48, POV.59 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:W.1029, A:A.1032, A:I.1035, D:L.863, D:M.867, D:T.870, D:F.871 Hydrogen bonds: A:P.1027 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.11, POV.14, POV.30, POV.33 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.863, A:L.866, A:M.867, A:T.870, A:F.871, A:Y.972, B:W.1029, B:A.1032, B:I.1035 Hydrogen bonds: B:P.1027 DU0.46: 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.29, POV.32, POV.45, POV.49 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.1029, C:A.1032, C:I.1035, B:L.863, B:M.867, B:T.870 Hydrogen bonds: C:P.1027 DU0.61: 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.44, POV.47, POV.60 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.1029, D:A.1032, D:I.1035, C:L.863, C:L.866, C:M.867, C:T.870 Hydrogen bonds: D:P.1027

1 x CA: CALCIUM ION(Non-covalent)

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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