SMTL ID : 7mbv.1

Cryo-EM structure of zebrafish TRPM5 in the presence of 5 mM calcium and 0.5 mM NDNA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 1 residues within 4Å: Chain A: N.921 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.921 NAG.7: 1 residues within 4Å: Chain B: N.921 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.921 NAG.13: 1 residues within 4Å: Chain C: N.921 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.921 NAG.20: 1 residues within 4Å: Chain D: N.921 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.921

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.768, N.794, D.797 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.768, A:D.797 CA.3: 5 residues within 4Å: Chain A: E.212, C.324, D.333, D.336, E.337 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.212, A:C.324, A:D.333, A:E.337 CA.8: 3 residues within 4Å: Chain B: E.768, N.794, D.797 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.768, B:D.797 CA.9: 5 residues within 4Å: Chain B: E.212, C.324, D.333, D.336, E.337 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.212, B:C.324, B:D.333, B:E.337 CA.14: 3 residues within 4Å: Chain C: E.768, N.794, D.797 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.768, C:D.797 CA.15: 5 residues within 4Å: Chain C: E.212, C.324, D.333, D.336, E.337 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.212, C:C.324, C:D.333, C:E.337 CA.21: 3 residues within 4Å: Chain D: E.768, N.794, D.797 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.768, D:D.797 CA.22: 5 residues within 4Å: Chain D: E.212, C.324, D.333, D.336, E.337 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.212, D:C.324, D:D.333, D:E.337

4 x YUS: N'-[(E)-(3,4-dimethoxyphenyl)methylidene]-2-(naphthalen-1-yl)acetohydrazide(Non-covalent)

YUS.4: 11 residues within 4Å: Chain A: N.792, W.793, C.796, L.833, I.836, I.849, V.852, E.853 Chain D: F.865, W.869, L.961 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.792, A:W.793, A:W.793, A:W.793, A:L.833, A:I.849, A:V.852 Hydrogen bonds: A:E.853, A:E.853 YUS.10: 11 residues within 4Å: Chain A: F.865, W.869, L.961 Chain B: N.792, W.793, C.796, L.833, I.836, I.849, V.852, E.853 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:N.792, B:W.793, B:W.793, B:W.793, B:L.833, B:I.849, B:V.852 Hydrogen bonds: B:E.853, B:E.853 YUS.16: 10 residues within 4Å: Chain B: F.865, W.869 Chain C: N.792, W.793, C.796, L.833, I.836, I.849, V.852, E.853 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.792, C:W.793, C:W.793, C:W.793, C:L.833, C:I.849, C:V.852 Hydrogen bonds: C:E.853, C:E.853 YUS.23: 10 residues within 4Å: Chain C: F.865, W.869 Chain D: N.792, W.793, C.796, L.833, I.836, I.849, V.852, E.853 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:N.792, D:W.793, D:W.793, D:W.793, D:L.833, D:I.849, D:V.852 Hydrogen bonds: D:E.853, D:E.853

4 x YUV: (25R)-14beta,17beta-spirost-5-en-3beta-ol(Non-covalent)

YUV.5: 4 residues within 4Å: Chain A: I.888, D.889, F.892 Ligands: YUY.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.888, A:D.889, A:F.892, A:F.892 YUV.11: 4 residues within 4Å: Chain B: I.888, D.889, F.892 Ligands: YUY.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.888, B:D.889, B:F.892, B:F.892 YUV.17: 4 residues within 4Å: Chain C: I.888, D.889, F.892 Ligands: YUY.12 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.888, C:D.889, C:F.892, C:F.892 YUV.24: 4 residues within 4Å: Chain D: I.888, D.889, F.892 Ligands: YUY.18 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.888, D:D.889, D:F.892, D:F.892

4 x YUY: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside(Non-covalent)

YUY.6: 15 residues within 4Å: Chain A: A.914, A.915, M.917, I.940, W.944, I.947, L.948 Chain B: L.870, D.889, W.890, F.892, L.896, Y.897, Y.900 Ligands: YUV.11 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.870, B:F.892, B:L.896, B:Y.897, B:Y.900, A:W.944, A:I.947, A:I.947, A:L.948 Hydrogen bonds: B:D.889, B:W.890, A:A.914 YUY.12: 15 residues within 4Å: Chain B: A.914, A.915, M.917, I.940, W.944, I.947, L.948 Chain C: L.870, D.889, W.890, F.892, L.896, Y.897, Y.900 Ligands: YUV.17 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:W.944, B:I.947, B:I.947, B:L.948, C:L.870, C:F.892, C:L.896, C:Y.897, C:Y.900 Hydrogen bonds: B:A.914, C:D.889, C:W.890 YUY.18: 15 residues within 4Å: Chain C: A.914, A.915, M.917, I.940, W.944, I.947, L.948 Chain D: L.870, D.889, W.890, F.892, L.896, Y.897, Y.900 Ligands: YUV.24 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.870, D:F.892, D:L.896, D:Y.897, D:Y.900, C:W.944, C:I.947, C:I.947, C:L.948 Hydrogen bonds: D:D.889, D:W.890, C:A.914 YUY.19: 15 residues within 4Å: Chain A: L.870, D.889, W.890, F.892, L.896, Y.897, Y.900 Chain D: A.914, A.915, M.917, I.940, W.944, I.947, L.948 Ligands: YUV.5 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:L.870, A:F.892, A:L.896, A:Y.897, A:Y.900, D:W.944, D:I.947, D:I.947, D:L.948 Hydrogen bonds: A:D.889, A:W.890, D:A.914

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruan, Z. et al., Structures of the TRPM5 channel elucidate mechanisms of activation and inhibition. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-07-07

Peptides

Transient receptor potential melastatin 5: 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 melastatin 5

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