SMTL ID : 8si2.1

Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 23 residues within 4Å: Chain A: R.730, Y.922, I.969, V.973, V.989, M.990, G.993, K.994, A.997, Y.1040, V.1109, Q.1113 Chain B: V.1009, S.1012, F.1013, L.1075, V.1078, Y.1079, F.1081 Ligands: CLR.4, POV.7, POV.8, POV.21 Ligand excluded by PLIP POV.2: 7 residues within 4Å: Chain A: K.916, F.919, S.920, I.929 Ligands: POV.3, POV.6, POV.8 Ligand excluded by PLIP POV.3: 11 residues within 4Å: Chain A: I.932, V.936, L.940, D.953, N.954, H.955, V.956, A.959 Ligands: POV.2, POV.6, POV.9 Ligand excluded by PLIP POV.5: 10 residues within 4Å: Chain A: S.743, W.746, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.15 Ligand excluded by PLIP POV.6: 15 residues within 4Å: Chain A: Y.952, D.953, H.955, V.958, A.959, L.962 Chain B: P.1067, G.1068, W.1070 Ligands: POV.2, POV.3, CLR.4, POV.8, POV.22, POV.23 Ligand excluded by PLIP POV.7: 15 residues within 4Å: Chain A: V.996, M.999, F.1000, Y.1001, V.1003, M.1006, A.1007, I.1043 Chain B: F.1081 Chain D: N.982, Q.984 Ligands: POV.1, POV.8, POV.21, POV.57 Ligand excluded by PLIP POV.8: 17 residues within 4Å: Chain A: S.920, Y.922, V.925, S.933, I.963, L.966, N.967, F.970, A.997 Chain B: F.1074 Ligands: POV.1, POV.2, CLR.4, POV.6, POV.7, POV.21, POV.23 Ligand excluded by PLIP POV.9: 17 residues within 4Å: Chain A: F.893, A.896, I.897, V.900, W.918, T.928, I.931, I.932, F.935, G.939, L.940, G.943, A.944, K.945, V.956 Ligands: POV.3, POV.10 Ligand excluded by PLIP POV.10: 11 residues within 4Å: Chain A: V.883, W.886, I.889, A.890, F.893, F.938, F.942, P.1130, I.1133 Ligands: POV.9, POV.11 Ligand excluded by PLIP POV.11: 7 residues within 4Å: Chain A: L.860, A.861, V.883, P.1130, L.1131 Ligands: POV.10, POV.12 Ligand excluded by PLIP POV.12: 18 residues within 4Å: Chain A: L.860, A.861, G.864, M.867, L.868, F.871, V.875, K.876, Q.884, I.887, Y.891, P.1130 Chain B: E.1026, P.1027 Ligands: POV.11, POV.15, POV.36, DU0.37 Ligand excluded by PLIP POV.13: 7 residues within 4Å: Chain A: W.1029 Chain D: M.867 Ligands: DU0.14, POV.22, POV.23, POV.57, POV.72 Ligand excluded by PLIP POV.15: 20 residues within 4Å: Chain A: W.757, I.761, F.855, W.856, L.860, F.978, L.979, V.981, N.982, Q.983 Chain B: V.1004, A.1007, L.1008, L.1011 Ligands: POV.5, POV.12, POV.30, POV.36, POV.39, POV.41 Ligand excluded by PLIP POV.16: 18 residues within 4Å: Chain A: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Chain D: A.1007, W.1029, A.1032, K.1033, V.1036 Ligands: POV.18, POV.56, POV.61, POV.67, POV.68 Ligand excluded by PLIP POV.17: 3 residues within 4Å: Ligands: POV.18, POV.66, POV.73 Ligand excluded by PLIP POV.18: 13 residues within 4Å: Chain A: C.1055, C.1065, G.1066, W.1070 Chain D: W.1029 Ligands: POV.16, POV.17, POV.56, CLR.64, POV.66, POV.68, POV.73, DU0.74 Ligand excluded by PLIP POV.21: 18 residues within 4Å: Chain A: A.1007, W.1029, A.1032, K.1033, V.1036 Chain B: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.1, POV.7, POV.8, POV.23, POV.57 Ligand excluded by PLIP POV.22: 3 residues within 4Å: Ligands: POV.6, POV.13, POV.23 Ligand excluded by PLIP POV.23: 14 residues within 4Å: Chain A: W.1029 Chain B: C.1055, C.1065, G.1066, W.1070, F.1074 Ligands: CLR.4, POV.6, POV.8, POV.13, DU0.14, POV.21, POV.22, POV.57 Ligand excluded by PLIP POV.24: 23 residues within 4Å: Chain B: R.730, Y.922, I.969, V.973, V.989, M.990, G.993, K.994, A.997, Y.1040, V.1109, Q.1113 Chain C: V.1009, S.1012, F.1013, L.1075, V.1078, Y.1079, F.1081 Ligands: CLR.27, POV.30, POV.31, POV.39 Ligand excluded by PLIP POV.25: 7 residues within 4Å: Chain B: K.916, F.919, S.920, I.929 Ligands: POV.26, POV.29, POV.31 Ligand excluded by PLIP POV.26: 12 residues within 4Å: Chain B: I.929, I.932, V.936, L.940, D.953, N.954, H.955, V.956, A.959 Ligands: POV.25, POV.29, POV.32 Ligand excluded by PLIP POV.28: 10 residues within 4Å: Chain B: S.743, W.746, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.38 Ligand excluded by PLIP POV.29: 15 residues within 4Å: Chain B: Y.952, D.953, H.955, V.958, A.959, L.962 Chain C: P.1067, G.1068, W.1070 Ligands: POV.25, POV.26, CLR.27, POV.31, POV.40, POV.41 Ligand excluded by PLIP POV.30: 14 residues within 4Å: Chain A: N.982, Q.984 Chain B: V.996, M.999, F.1000, Y.1001, V.1003, M.1006, I.1043 Chain C: F.1081 Ligands: POV.15, POV.24, POV.31, POV.39 Ligand excluded by PLIP POV.31: 17 residues within 4Å: Chain B: S.920, Y.922, V.925, S.933, I.963, L.966, N.967, F.970, A.997 Chain C: F.1074 Ligands: POV.24, POV.25, CLR.27, POV.29, POV.30, POV.39, POV.41 Ligand excluded by PLIP POV.32: 17 residues within 4Å: Chain B: F.893, A.896, I.897, V.900, W.918, T.928, I.931, I.932, F.935, G.939, L.940, G.943, A.944, K.945, V.956 Ligands: POV.26, POV.33 Ligand excluded by PLIP POV.33: 11 residues within 4Å: Chain B: V.883, W.886, I.889, A.890, F.893, F.938, F.942, P.1130, I.1133 Ligands: POV.32, POV.34 Ligand excluded by PLIP POV.34: 8 residues within 4Å: Chain B: L.860, A.861, V.883, I.887, P.1130, L.1131 Ligands: POV.33, POV.35 Ligand excluded by PLIP POV.35: 18 residues within 4Å: Chain B: L.860, A.861, G.864, M.867, L.868, F.871, V.875, K.876, Q.884, I.887, Y.891, P.1130 Chain C: E.1026, P.1027 Ligands: POV.34, POV.38, POV.54, DU0.55 Ligand excluded by PLIP POV.36: 7 residues within 4Å: Chain A: M.867 Chain B: W.1029 Ligands: POV.12, POV.15, DU0.37, POV.40, POV.41 Ligand excluded by PLIP POV.38: 18 residues within 4Å: Chain B: W.757, I.761, F.855, W.856, F.978, L.979, V.981, N.982, Q.983 Chain C: V.1004, L.1008, L.1011 Ligands: POV.28, POV.35, POV.48, POV.54, POV.58, POV.60 Ligand excluded by PLIP POV.39: 18 residues within 4Å: Chain B: A.1007, W.1029, A.1032, K.1033, V.1036 Chain C: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.15, POV.24, POV.30, POV.31, POV.41 Ligand excluded by PLIP POV.40: 3 residues within 4Å: Ligands: POV.29, POV.36, POV.41 Ligand excluded by PLIP POV.41: 13 residues within 4Å: Chain B: W.1029 Chain C: C.1055, C.1065, G.1066, W.1070 Ligands: POV.15, CLR.27, POV.29, POV.31, POV.36, DU0.37, POV.39, POV.40 Ligand excluded by PLIP POV.42: 23 residues within 4Å: Chain C: R.730, Y.922, I.969, V.973, V.989, M.990, G.993, K.994, A.997, Y.1040, V.1109, Q.1113 Chain D: V.1009, S.1012, F.1013, L.1075, V.1078, Y.1079, F.1081 Ligands: CLR.45, POV.48, POV.49, POV.58 Ligand excluded by PLIP POV.43: 7 residues within 4Å: Chain C: K.916, F.919, S.920, I.929 Ligands: POV.44, POV.47, POV.49 Ligand excluded by PLIP POV.44: 12 residues within 4Å: Chain C: I.929, I.932, V.936, L.940, D.953, N.954, H.955, V.956, A.959 Ligands: POV.43, POV.47, POV.50 Ligand excluded by PLIP POV.46: 10 residues within 4Å: Chain C: S.743, W.746, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.56 Ligand excluded by PLIP POV.47: 16 residues within 4Å: Chain C: Y.952, D.953, H.955, V.958, A.959, L.962, L.966 Chain D: P.1067, G.1068, W.1070 Ligands: POV.43, POV.44, CLR.45, POV.49, POV.59, POV.60 Ligand excluded by PLIP POV.48: 15 residues within 4Å: Chain B: N.982, Q.984 Chain C: V.996, M.999, F.1000, Y.1001, V.1003, M.1006, A.1007, I.1043 Chain D: F.1081 Ligands: POV.38, POV.42, POV.49, POV.58 Ligand excluded by PLIP POV.49: 17 residues within 4Å: Chain C: S.920, Y.922, V.925, S.933, I.963, L.966, N.967, F.970, A.997 Chain D: F.1074 Ligands: POV.42, POV.43, CLR.45, POV.47, POV.48, POV.58, POV.60 Ligand excluded by PLIP POV.50: 17 residues within 4Å: Chain C: F.893, A.896, I.897, V.900, W.918, T.928, I.931, I.932, F.935, G.939, L.940, G.943, A.944, K.945, V.956 Ligands: POV.44, POV.51 Ligand excluded by PLIP POV.51: 11 residues within 4Å: Chain C: V.883, W.886, I.889, A.890, F.893, F.938, F.942, P.1130, I.1133 Ligands: POV.50, POV.52 Ligand excluded by PLIP POV.52: 8 residues within 4Å: Chain C: L.860, A.861, V.883, I.887, P.1130, L.1131 Ligands: POV.51, POV.53 Ligand excluded by PLIP POV.53: 18 residues within 4Å: Chain C: L.860, A.861, G.864, M.867, L.868, F.871, V.875, K.876, Q.884, I.887, Y.891, P.1130 Chain D: E.1026, P.1027 Ligands: POV.52, POV.56, POV.73, DU0.74 Ligand excluded by PLIP POV.54: 7 residues within 4Å: Chain B: M.867 Chain C: W.1029 Ligands: POV.35, POV.38, DU0.55, POV.59, POV.60 Ligand excluded by PLIP POV.56: 19 residues within 4Å: Chain C: W.757, I.761, F.855, W.856, L.860, F.978, L.979, V.981, N.982, Q.983 Chain D: V.1004, L.1008, L.1011 Ligands: POV.16, POV.18, POV.46, POV.53, POV.67, POV.73 Ligand excluded by PLIP POV.57: 20 residues within 4Å: Chain A: V.1004, A.1007, L.1008, L.1011 Chain D: W.757, I.761, F.855, W.856, L.860, F.978, L.979, V.981, N.982, Q.983 Ligands: POV.7, POV.13, POV.21, POV.23, POV.65, POV.72 Ligand excluded by PLIP POV.58: 18 residues within 4Å: Chain C: A.1007, W.1029, A.1032, K.1033, V.1036 Chain D: D.1053, C.1055, A.1056, N.1057, W.1070, P.1073, F.1074, A.1077 Ligands: POV.38, POV.42, POV.48, POV.49, POV.60 Ligand excluded by PLIP POV.59: 3 residues within 4Å: Ligands: POV.47, POV.54, POV.60 Ligand excluded by PLIP POV.60: 13 residues within 4Å: Chain C: W.1029 Chain D: C.1055, C.1065, G.1066, W.1070 Ligands: POV.38, CLR.45, POV.47, POV.49, POV.54, DU0.55, POV.58, POV.59 Ligand excluded by PLIP POV.61: 23 residues within 4Å: Chain A: V.1009, S.1012, F.1013, L.1075, V.1078, Y.1079, F.1081 Chain D: R.730, Y.922, I.969, V.973, V.989, M.990, G.993, K.994, A.997, Y.1040, V.1109, Q.1113 Ligands: POV.16, CLR.64, POV.67, POV.68 Ligand excluded by PLIP POV.62: 7 residues within 4Å: Chain D: K.916, F.919, S.920, I.929 Ligands: POV.63, POV.66, POV.68 Ligand excluded by PLIP POV.63: 11 residues within 4Å: Chain D: I.932, V.936, L.940, D.953, N.954, H.955, V.956, A.959 Ligands: POV.62, POV.66, POV.69 Ligand excluded by PLIP POV.65: 10 residues within 4Å: Chain D: S.743, W.746, A.980, V.981, M.990, W.1110, Q.1113, R.1114, F.1117 Ligands: POV.57 Ligand excluded by PLIP POV.66: 15 residues within 4Å: Chain A: P.1067, G.1068, W.1070 Chain D: Y.952, D.953, H.955, V.958, A.959, L.962 Ligands: POV.17, POV.18, POV.62, POV.63, CLR.64, POV.68 Ligand excluded by PLIP POV.67: 14 residues within 4Å: Chain A: F.1081 Chain C: N.982, Q.984 Chain D: V.996, M.999, F.1000, Y.1001, V.1003, M.1006, I.1043 Ligands: POV.16, POV.56, POV.61, POV.68 Ligand excluded by PLIP POV.68: 17 residues within 4Å: Chain A: F.1074 Chain D: S.920, Y.922, V.925, S.933, I.963, L.966, N.967, F.970, A.997 Ligands: POV.16, POV.18, POV.61, POV.62, CLR.64, POV.66, POV.67 Ligand excluded by PLIP POV.69: 17 residues within 4Å: Chain D: F.893, A.896, I.897, V.900, W.918, T.928, I.931, I.932, F.935, G.939, L.940, G.943, A.944, K.945, V.956 Ligands: POV.63, POV.70 Ligand excluded by PLIP POV.70: 11 residues within 4Å: Chain D: V.883, W.886, I.889, A.890, F.893, F.938, F.942, P.1130, I.1133 Ligands: POV.69, POV.71 Ligand excluded by PLIP POV.71: 8 residues within 4Å: Chain D: L.860, A.861, V.883, I.887, P.1130, L.1131 Ligands: POV.70, POV.72 Ligand excluded by PLIP POV.72: 18 residues within 4Å: Chain A: E.1026, P.1027 Chain D: L.860, A.861, G.864, M.867, L.868, F.871, V.875, K.876, Q.884, I.887, Y.891, P.1130 Ligands: POV.13, DU0.14, POV.57, POV.71 Ligand excluded by PLIP POV.73: 7 residues within 4Å: Chain C: M.867 Chain D: W.1029 Ligands: POV.17, POV.18, POV.53, POV.56, DU0.74 Ligand excluded by PLIP

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 12 residues within 4Å: Chain A: Y.922, L.966, I.969, F.970, V.973 Chain B: W.1070, L.1071, L.1075 Ligands: POV.1, POV.6, POV.8, POV.23 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.1070, B:W.1070, B:L.1071, B:L.1075, A:L.966, A:I.969, A:F.970, A:F.970 Hydrogen bonds: A:Y.922 CLR.27: 12 residues within 4Å: Chain B: Y.922, L.966, I.969, F.970, V.973 Chain C: W.1070, L.1071, L.1075 Ligands: POV.24, POV.29, POV.31, POV.41 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.966, 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 CLR.45: 12 residues within 4Å: Chain C: Y.922, L.966, I.969, F.970, V.973 Chain D: W.1070, L.1071, L.1075 Ligands: POV.42, POV.47, POV.49, POV.60 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:W.1070, D:W.1070, D:L.1071, D:L.1075, C:L.966, C:I.969, C:F.970, C:F.970 Hydrogen bonds: C:Y.922 CLR.64: 12 residues within 4Å: Chain A: W.1070, L.1071, L.1075 Chain D: Y.922, L.966, I.969, F.970, V.973 Ligands: POV.18, POV.61, POV.66, POV.68 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:W.1070, A:W.1070, A:L.1071, A:L.1075, D:L.966, D:I.969, 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)

DU0.14: 12 residues within 4Å: Chain A: P.1027, S.1028, W.1029, A.1032, I.1035 Chain D: M.867, T.870, F.871, Y.972 Ligands: POV.13, POV.23, POV.72 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.1029, A:A.1032, A:I.1035, D:F.871 DU0.37: 12 residues within 4Å: Chain A: M.867, T.870, F.871, Y.972 Chain B: P.1027, S.1028, W.1029, A.1032, I.1035 Ligands: POV.12, POV.36, POV.41 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.871, B:W.1029, B:A.1032, B:I.1035 DU0.55: 12 residues within 4Å: Chain B: M.867, T.870, F.871, Y.972 Chain C: P.1027, S.1028, W.1029, A.1032, I.1035 Ligands: POV.35, POV.54, POV.60 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.871, C:W.1029, C:A.1032, C:I.1035 DU0.74: 12 residues within 4Å: Chain C: M.867, T.870, F.871, Y.972 Chain D: P.1027, S.1028, W.1029, A.1032, I.1035 Ligands: POV.18, POV.53, POV.73 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.1029, D:A.1032, D:I.1035, C:F.871

2 x NA: SODIUM ION(Non-functional Binders)

NA.19: 5 residues within 4Å: Chain A: G.1045 Chain B: G.1045 Chain C: G.1045 Chain D: G.1045 Ligands: NA.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.1045 NA.20: 5 residues within 4Å: Chain A: G.1045 Chain B: G.1045 Chain C: G.1045 Chain D: G.1045 Ligands: NA.19 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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