SMTL ID : 6bwi.1

3.7 angstrom cryoEM structure of full length human TRPM4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: G.777 Chain C: G.777 Chain D: G.777 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.777, C:G.777 NA.2: 4 residues within 4Å: Chain A: S.845 Chain B: S.845 Chain C: S.845 Chain D: S.845 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:S.845, A:S.845, A:S.845, B:S.845, C:S.845 NA.3: 4 residues within 4Å: Chain A: S.845 Chain B: S.845 Chain C: S.845 Chain D: S.845 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.845 NA.11: 6 residues within 4Å: Chain A: G.777 Chain B: G.777, Q.778 Chain C: G.777 Chain D: G.777, Q.778 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.778 NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

24 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)(Covalent)

Y01.4: 11 residues within 4Å: Chain A: P.761, L.764, R.765, F.768, Q.808 Chain B: D.785, N.818, W.819, V.822 Ligands: Y01.9, Y01.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.761, A:R.765, A:F.768 Y01.5: 2 residues within 4Å: Chain A: Y.816 Chain D: L.691 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.816, D:L.691 Y01.6: 13 residues within 4Å: Chain A: F.737, V.826, I.827, L.830, L.835 Chain D: W.665, L.708, I.721, S.725, F.732, L.735 Ligands: Y01.27, Y01.32 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:V.826, A:I.827, A:I.827, A:L.830, A:L.835, D:W.665, D:L.708, D:F.732, D:L.735, D:L.735 Y01.7: 9 residues within 4Å: Chain A: W.481, I.491, V.495, F.584, M.585, V.588, V.589, L.592, N.714 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.491, A:I.491, A:V.495, A:V.588, A:V.589, A:L.592 Y01.8: 10 residues within 4Å: Chain A: S.664, W.665, C.668, I.698, M.701, V.702, V.705, S.725 Chain B: W.741 Ligands: Y01.9 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.665, A:I.698, A:V.702, A:V.705, B:W.741 Hydrogen bonds: A:S.664, A:S.664, A:S.725 Salt bridges: A:K.726 Y01.9: 10 residues within 4Å: Chain A: I.721, S.725, F.732, L.735 Chain B: V.826, I.827, L.830, L.835 Ligands: Y01.4, Y01.8 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.826, B:I.827, B:I.827, B:I.827, B:L.830, B:L.835, A:I.721, A:F.732, A:L.735 Y01.13: 4 residues within 4Å: Chain A: D.759, L.764 Chain B: W.819 Ligands: Y01.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.764 Y01.14: 8 residues within 4Å: Chain B: P.761, L.764, R.765, F.768 Chain C: A.787, N.818, V.822 Ligands: Y01.20 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.761, B:F.768, C:V.822, C:V.822 Y01.15: 2 residues within 4Å: Chain A: L.691 Chain B: Y.816 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.816, A:L.691 Y01.16: 8 residues within 4Å: Chain B: W.481, I.491, V.495, F.584, V.588, V.589, L.592, N.714 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.491, B:V.495, B:V.588, B:V.589 Y01.17: 8 residues within 4Å: Chain B: S.664, W.665, C.668, I.698, M.701, V.705 Chain C: L.824 Ligands: Y01.18 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.665, B:I.698, B:V.705, B:V.705, C:L.824 Salt bridges: B:K.726 Y01.18: 12 residues within 4Å: Chain B: W.665, L.708, I.721, S.725, F.732, L.735 Chain C: F.737, V.826, I.827, L.830, L.835 Ligands: Y01.17 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:W.665, B:L.708, B:F.732, B:F.732, B:L.735, C:V.826, C:I.827, C:I.827, C:I.827, C:L.830, C:L.835 Y01.20: 5 residues within 4Å: Chain B: D.759, P.761, L.764 Chain C: W.819 Ligands: Y01.14 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.819, B:P.761, B:L.764 Y01.21: 10 residues within 4Å: Chain C: P.761, L.764, R.765, F.768 Chain D: D.785, H.791, N.818, W.819, V.822 Ligands: Y01.26 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.761, C:F.768 Salt bridges: D:H.791 Y01.22: 2 residues within 4Å: Chain B: L.691 Chain C: Y.816 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.691 Y01.23: 7 residues within 4Å: Chain C: W.481, I.491, V.495, F.584, V.588, V.589, N.714 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.491, C:I.491, C:V.495, C:V.588, C:V.589 Y01.24: 8 residues within 4Å: Chain C: S.664, W.665, C.668, I.698, M.701, V.705 Chain D: L.824 Ligands: Y01.31 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.665, C:W.665, C:I.698, C:V.705, C:V.705 Hydrogen bonds: C:S.664 Y01.26: 4 residues within 4Å: Chain C: P.761, L.764 Chain D: W.819 Ligands: Y01.21 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.761, C:L.764, D:W.819 Y01.27: 11 residues within 4Å: Chain A: H.791, N.818, V.822, L.823 Chain D: L.742, P.761, L.764, R.765, F.768 Ligands: Y01.6, Y01.28 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.742, D:P.761, D:F.768, A:L.823 Salt bridges: A:H.791 Y01.28: 4 residues within 4Å: Chain A: W.819 Chain D: P.761, L.764 Ligands: Y01.27 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.819, D:P.761, D:L.764 Y01.29: 2 residues within 4Å: Chain C: L.691 Chain D: Y.816 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.691 Y01.30: 10 residues within 4Å: Chain D: W.481, I.491, V.495, F.584, V.588, V.589, L.592, L.593, V.713, N.714 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.491, D:V.495, D:F.584, D:V.588, D:V.589, D:L.592, D:L.593 Y01.31: 12 residues within 4Å: Chain C: W.665, L.708, I.721, S.725, F.732, L.735 Chain D: F.737, V.826, I.827, L.830, L.835 Ligands: Y01.24 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.826, D:I.827, D:L.835, C:W.665, C:L.708, C:F.732, C:L.735, C:L.735 Y01.32: 11 residues within 4Å: Chain A: L.820, L.823, L.824, I.827 Chain D: S.664, W.665, C.668, I.698, M.701, V.705 Ligands: Y01.6 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain D Hydrophobic interactions: A:L.820, A:L.823, A:L.824, A:I.827, D:W.665, D:W.665, D:W.665, D:I.698, D:I.698, D:M.701, D:V.705, D:V.705 Hydrogen bonds: D:S.664

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

NAG.10: 1 residues within 4Å: Chain A: N.793 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.793, A:N.793 NAG.19: 1 residues within 4Å: Chain B: N.793 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.793, B:N.793 NAG.25: 1 residues within 4Å: Chain C: N.793 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.793 NAG.33: 1 residues within 4Å: Chain D: N.793 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.793

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, J. et al., Structure of full-length human TRPM4. Proc.Natl.Acad.Sci.USA (2018)

Release Date

2018-12-19

Peptides

Transient receptor potential cation channel subfamily M member 4: 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 4