SMTL ID : 8srg.1

Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)

RP5.1: 17 residues within 4Å: Chain A: D.1330, R.1360, I.1368, G.1370, G.1371, F.1372, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: AMP.2, MG.5, MG.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.1330, A:G.1370, A:F.1372, A:D.1426 Salt bridges: A:R.1360, A:R.1428, A:R.1428 RP5.10: 17 residues within 4Å: Chain B: D.1330, R.1360, I.1368, G.1370, G.1371, F.1372, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: AMP.11, MG.14, MG.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.1330, B:G.1370, B:F.1372, B:D.1426 Salt bridges: B:R.1360, B:R.1428, B:R.1428 RP5.19: 17 residues within 4Å: Chain C: D.1330, R.1360, I.1368, G.1370, G.1371, F.1372, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: AMP.20, MG.23, MG.24 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.1330, C:G.1370, C:F.1372, C:D.1426 Salt bridges: C:R.1360, C:R.1428, C:R.1428 RP5.30: 17 residues within 4Å: Chain D: D.1330, R.1360, I.1368, G.1370, G.1371, F.1372, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: AMP.31, MG.34, MG.35 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.1330, D:G.1370, D:F.1372, D:D.1426 Salt bridges: D:R.1360, D:R.1428, D:R.1428

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 10 residues within 4Å: Chain A: W.1264, L.1319, L.1320, G.1321, N.1326, R.1360, F.1372, D.1460 Ligands: RP5.1, MG.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.1264, A:G.1321, A:N.1326, A:R.1360, A:D.1460 pi-Stacking: A:W.1264, A:F.1372 AMP.11: 10 residues within 4Å: Chain B: W.1264, L.1319, L.1320, G.1321, N.1326, R.1360, F.1372, D.1460 Ligands: RP5.10, MG.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.1264, B:G.1321, B:N.1326, B:R.1360, B:D.1460 pi-Stacking: B:W.1264, B:F.1372 AMP.20: 10 residues within 4Å: Chain C: W.1264, L.1319, L.1320, G.1321, N.1326, R.1360, F.1372, D.1460 Ligands: RP5.19, MG.24 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.1264, C:G.1321, C:N.1326, C:R.1360, C:D.1460 pi-Stacking: C:W.1264, C:F.1372 AMP.31: 10 residues within 4Å: Chain D: W.1264, L.1319, L.1320, G.1321, N.1326, R.1360, F.1372, D.1460 Ligands: RP5.30, MG.35 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:W.1264, D:G.1321, D:N.1326, D:R.1360, D:D.1460 pi-Stacking: D:W.1264, D:F.1372

16 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.850 MG.4: 4 residues within 4Å: Chain A: L.621, I.622, G.623, E.1114 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.621, A:G.623, A:E.1114, A:E.1114 MG.5: 4 residues within 4Å: Chain A: G.1370, E.1390 Ligands: RP5.1, MG.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.1370, A:E.1390, A:E.1390 MG.6: 5 residues within 4Å: Chain A: E.1390, D.1460 Ligands: RP5.1, AMP.2, MG.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.1390, A:D.1460 MG.12: 4 residues within 4Å: Chain B: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.850 MG.13: 4 residues within 4Å: Chain B: L.621, I.622, G.623, E.1114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:L.621, B:G.623, B:E.1114, B:E.1114 MG.14: 4 residues within 4Å: Chain B: G.1370, E.1390 Ligands: RP5.10, MG.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.1370, B:E.1390, B:E.1390 MG.15: 5 residues within 4Å: Chain B: E.1390, D.1460 Ligands: RP5.10, AMP.11, MG.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.1390, B:D.1460 MG.21: 4 residues within 4Å: Chain C: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.850 MG.22: 4 residues within 4Å: Chain C: L.621, I.622, G.623, E.1114 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:L.621, C:G.623, C:E.1114, C:E.1114 MG.23: 4 residues within 4Å: Chain C: G.1370, E.1390 Ligands: RP5.19, MG.24 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:G.1370, C:E.1390, C:E.1390 MG.24: 5 residues within 4Å: Chain C: E.1390, D.1460 Ligands: RP5.19, AMP.20, MG.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.1390, C:D.1460 MG.32: 4 residues within 4Å: Chain D: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.850 MG.33: 4 residues within 4Å: Chain D: L.621, I.622, G.623, E.1114 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:L.621, D:G.623, D:E.1114, D:E.1114 MG.34: 4 residues within 4Å: Chain D: G.1370, E.1390 Ligands: RP5.30, MG.35 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.1370, D:E.1390, D:E.1390 MG.35: 5 residues within 4Å: Chain D: E.1390, D.1460 Ligands: RP5.30, AMP.31, MG.34 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.1390, D:D.1460

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 8 residues within 4Å: Chain A: L.878, V.898, I.902, F.905 Chain D: E.1009, T.1010, M.1013 Ligands: CLR.29 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:T.1010, A:V.898, A:I.902, A:I.902, A:F.905, A:F.905, A:F.905 CLR.8: 13 residues within 4Å: Chain A: F.1003, R.1012, P.1015, F.1016 Chain B: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Ligands: CLR.9 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.945, B:L.946, B:L.949, B:F.976, B:Y.979, B:Y.979, B:Y.979, A:F.1003, A:P.1015, A:F.1016, A:F.1016 Hydrogen bonds: A:R.1012, A:R.1012 CLR.9: 6 residues within 4Å: Chain A: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.8, CLR.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.1012, A:F.1016, A:F.1016, A:F.1016 CLR.16: 8 residues within 4Å: Chain A: E.1009, T.1010, M.1013 Chain B: L.878, V.898, I.902, F.905 Ligands: CLR.9 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.898, B:I.902, B:I.902, B:F.905, B:F.905, B:F.905, A:T.1010 CLR.17: 13 residues within 4Å: Chain B: F.1003, R.1012, P.1015, F.1016 Chain C: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Ligands: CLR.18 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.1003, B:P.1015, B:F.1016, B:F.1016, C:L.945, C:L.946, C:L.949, C:F.976, C:Y.979, C:Y.979, C:Y.979 Hydrogen bonds: B:R.1012, B:R.1012 CLR.18: 6 residues within 4Å: Chain B: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.17, CLR.25 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.1012, B:F.1016, B:F.1016, B:F.1016 CLR.25: 8 residues within 4Å: Chain B: E.1009, T.1010, M.1013 Chain C: L.878, V.898, I.902, F.905 Ligands: CLR.18 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.898, C:I.902, C:I.902, C:F.905, C:F.905, C:F.905, B:T.1010 CLR.26: 13 residues within 4Å: Chain C: F.1003, R.1012, P.1015, F.1016 Chain D: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Ligands: CLR.27 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:F.1003, C:P.1015, C:F.1016, C:F.1016, D:L.945, D:L.946, D:L.949, D:F.976, D:Y.979, D:Y.979, D:Y.979 Hydrogen bonds: C:R.1012, C:R.1012 CLR.27: 6 residues within 4Å: Chain C: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.26, CLR.36 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.1012, C:F.1016, C:F.1016, C:F.1016 CLR.28: 13 residues within 4Å: Chain A: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Chain D: F.1003, R.1012, P.1015, F.1016 Ligands: CLR.29 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:L.945, A:L.946, A:L.949, A:F.976, A:Y.979, A:Y.979, A:Y.979, D:F.1003, D:P.1015, D:F.1016, D:F.1016 Hydrogen bonds: D:R.1012, D:R.1012 CLR.29: 6 residues within 4Å: Chain D: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.7, CLR.28 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:R.1012, D:F.1016, D:F.1016, D:F.1016 CLR.36: 8 residues within 4Å: Chain C: E.1009, T.1010, M.1013 Chain D: L.878, V.898, I.902, F.905 Ligands: CLR.27 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.898, D:I.902, D:I.902, D:F.905, D:F.905, D:F.905, C:T.1010

Links

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Citation

Huang, Y. et al., Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. To Be Published

Release Date

2024-05-15

Peptides

TRPM2 chanzyme: 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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TRPM2 chanzyme

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