SMTL ID : 7usw.1

Structure of Expanded C. elegans TMC-1 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-2-2-2-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.683, T.687, L.760 No protein-ligand interaction detected (PLIP) CA.2: 4 residues within 4Å: Chain A: D.695, F.723, R.764, N.772 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.695 CA.29: 3 residues within 4Å: Chain B: D.683, T.687, L.760 No protein-ligand interaction detected (PLIP) CA.30: 4 residues within 4Å: Chain B: D.695, F.723, R.764, N.772 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.695 CA.57: 4 residues within 4Å: Chain C: D.132, D.134, L.136, D.141 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.132, C:D.132, C:D.134, C:L.136, C:D.141 CA.58: 4 residues within 4Å: Chain C: D.171, D.175, S.177, N.179 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.171, C:S.177 CA.64: 4 residues within 4Å: Chain E: D.132, D.134, L.136, D.141 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.132, E:D.132, E:D.134, E:L.136, E:D.141 CA.65: 3 residues within 4Å: Chain E: D.171, S.177, N.179 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.171, E:S.177

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.3: 17 residues within 4Å: Chain A: F.142, K.146, Y.148, L.149, I.150, P.151, E.153, R.175, W.176, V.178, F.179, I.182, Y.276, K.284 Chain C: E.114 Ligands: D12.8, ZFC.19 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.142, A:I.150, A:F.179, A:F.179, A:I.182, A:Y.276 Hydrogen bonds: A:R.175, C:E.114 Salt bridges: A:R.175, A:K.284 PEE.31: 17 residues within 4Å: Chain B: F.142, K.146, Y.148, L.149, I.150, P.151, E.153, R.175, W.176, V.178, F.179, I.182, Y.276, K.284 Chain E: E.114 Ligands: D12.36, ZFC.48 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:F.142, B:I.150, B:F.179, B:F.179, B:I.182, B:Y.276 Hydrogen bonds: B:R.175, E:E.114 Salt bridges: B:R.175, B:K.284

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.4: 19 residues within 4Å: Chain A: K.155, R.158, L.684, I.685, I.688, L.692, Y.762, I.763, W.766 Chain D: L.36, I.39, V.40, C.43, C.44, M.46, R.47 Ligands: ZFC.6, PLM.62, PLM.63 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.684, A:I.685, A:L.692, A:L.692, A:I.763, D:L.36, D:L.36, D:I.39 Hydrogen bonds: A:R.158, A:Y.762, D:M.46 Salt bridges: A:K.155 3PE.32: 17 residues within 4Å: Chain B: K.155, R.158, L.684, I.685, I.688, L.692, Y.762, I.763, W.766 Chain F: L.36, I.39, V.40, C.44, M.46 Ligands: ZFC.34, PLM.69, PLM.70 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain F Hydrophobic interactions: B:L.684, B:I.685, B:L.692, B:L.692, B:I.763, F:L.36, F:L.36, F:I.39 Hydrogen bonds: B:R.158, B:Y.762, F:M.46 Salt bridges: B:K.155

34 x ZFC: undecan-1-ol(Non-covalent)(Covalent)

ZFC.5: 1 residues within 4Å: Chain A: A.808 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.808 ZFC.6: 6 residues within 4Å: Chain A: V.680, L.684, I.752, K.756 Ligands: 3PE.4, D12.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.680, A:L.684, A:I.752, A:K.756 ZFC.14: 3 residues within 4Å: Chain A: L.797, L.798 Chain B: F.860 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.797, A:L.798, B:F.860 ZFC.15: 5 residues within 4Å: Chain A: L.433, S.784, N.786, F.787, I.794 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.433, A:F.787, A:F.787, A:I.794 ZFC.16: 5 residues within 4Å: Chain A: I.441, I.444, F.445, F.448, F.805 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.441, A:I.444, A:F.445, A:F.448, A:F.805 ZFC.17: 5 residues within 4Å: Chain A: N.360, T.423, R.426, R.431 Ligands: ZFC.25 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.431 ZFC.18: 2 residues within 4Å: Chain A: G.368 Ligands: R16.11 No protein-ligand interaction detected (PLIP) ZFC.19: 6 residues within 4Å: Chain A: M.183, I.187, V.190, F.191, Y.276 Ligands: PEE.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.190, A:F.191, A:Y.276 ZFC.20: 6 residues within 4Å: Chain A: F.191, P.195, L.198, I.258, Y.260 Ligands: ZFC.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.191, A:P.195, A:P.195, A:L.198, A:I.258, A:Y.260 ZFC.21: 3 residues within 4Å: Chain A: I.258 Ligands: CLR.10, ZFC.20 No protein-ligand interaction detected (PLIP) ZFC.22: 1 residues within 4Å: Chain A: E.832 No protein-ligand interaction detected (PLIP) ZFC.23: 1 residues within 4Å: Chain A: F.686 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.686 ZFC.25: 5 residues within 4Å: Chain A: R.426, G.430, I.434, T.437 Ligands: ZFC.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.434, A:I.434 ZFC.26: 3 residues within 4Å: Chain A: R.422, R.426, S.782 No protein-ligand interaction detected (PLIP) ZFC.33: 1 residues within 4Å: Chain B: A.808 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.808 ZFC.34: 6 residues within 4Å: Chain B: V.680, L.684, I.752, K.756 Ligands: 3PE.32, D12.37 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.680, B:L.684, B:I.752, B:K.756 ZFC.43: 3 residues within 4Å: Chain A: F.860 Chain B: L.797, L.798 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.797, B:L.798, A:F.860 ZFC.44: 5 residues within 4Å: Chain B: L.433, S.784, N.786, F.787, I.794 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.433, B:F.787, B:F.787, B:I.794 ZFC.45: 5 residues within 4Å: Chain B: I.441, I.444, F.445, F.448, F.805 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.441, B:I.444, B:F.445, B:F.448, B:F.805 ZFC.46: 5 residues within 4Å: Chain B: N.360, T.423, R.426, R.431 Ligands: ZFC.54 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.431 ZFC.47: 2 residues within 4Å: Chain B: G.368 Ligands: R16.40 No protein-ligand interaction detected (PLIP) ZFC.48: 6 residues within 4Å: Chain B: M.183, I.187, V.190, F.191, Y.276 Ligands: PEE.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.190, B:F.191, B:Y.276 ZFC.49: 5 residues within 4Å: Chain B: F.191, P.195, L.198, I.258 Ligands: ZFC.50 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.191, B:P.195, B:P.195, B:L.198, B:I.258 ZFC.50: 3 residues within 4Å: Chain B: I.258 Ligands: CLR.38, ZFC.49 No protein-ligand interaction detected (PLIP) ZFC.51: 1 residues within 4Å: Chain B: E.832 No protein-ligand interaction detected (PLIP) ZFC.52: 1 residues within 4Å: Chain B: F.686 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.686 ZFC.54: 5 residues within 4Å: Chain B: R.426, G.430, I.434, T.437 Ligands: ZFC.46 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.434, B:I.434 ZFC.55: 3 residues within 4Å: Chain B: R.422, R.426, S.782 No protein-ligand interaction detected (PLIP) ZFC.59: 2 residues within 4Å: Chain D: M.26, A.29 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.29 ZFC.60: 3 residues within 4Å: Chain D: A.29, G.32, G.33 No protein-ligand interaction detected (PLIP) ZFC.61: 3 residues within 4Å: Chain D: L.36, V.40 Ligands: PLM.62 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.36 ZFC.66: 2 residues within 4Å: Chain F: M.26, A.29 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:A.29 ZFC.67: 3 residues within 4Å: Chain F: A.29, G.32, G.33 No protein-ligand interaction detected (PLIP) ZFC.68: 3 residues within 4Å: Chain F: L.36, V.40 Ligands: PLM.69 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.36

12 x D12: DODECANE(Non-covalent)

D12.7: 1 residues within 4Å: Chain A: V.193 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.193 D12.8: 4 residues within 4Å: Chain A: P.151, W.152, Y.762 Ligands: PEE.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.151, A:W.152, A:W.152 D12.9: 2 residues within 4Å: Chain A: Y.234 Ligands: ZFC.6 No protein-ligand interaction detected (PLIP) D12.12: 3 residues within 4Å: Chain A: I.694, R.698, F.717 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.694, A:R.698, A:F.717 D12.13: 4 residues within 4Å: Chain A: I.371, I.375, F.445, E.449 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.371, A:F.445, A:F.445 D12.24: 5 residues within 4Å: Chain A: L.228, W.232, H.233, L.389, F.390 No protein-ligand interaction detected (PLIP) D12.35: 2 residues within 4Å: Chain B: L.189, V.193 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.189, B:V.193 D12.36: 4 residues within 4Å: Chain B: P.151, W.152, Y.762 Ligands: PEE.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.151, B:W.152, B:W.152 D12.37: 3 residues within 4Å: Chain B: V.231, Y.234 Ligands: ZFC.34 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.231 D12.41: 3 residues within 4Å: Chain B: I.694, R.698, F.717 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.694, B:R.698, B:F.717 D12.42: 3 residues within 4Å: Chain B: I.371, I.375, F.445 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.371, B:F.445, B:F.445 D12.53: 5 residues within 4Å: Chain B: L.228, W.232, H.233, L.389, F.390 No protein-ligand interaction detected (PLIP)

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.10: 10 residues within 4Å: Chain A: F.191, K.259, Y.260, A.261, L.264, A.265, M.268, T.272, E.832 Ligands: ZFC.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.191, A:F.191, A:F.191, A:Y.260, A:M.268, A:T.272 CLR.38: 10 residues within 4Å: Chain B: F.191, K.259, Y.260, A.261, L.264, A.265, M.268, T.272, E.832 Ligands: ZFC.50 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.191, B:F.191, B:F.191, B:Y.260, B:M.268, B:T.272

4 x R16: HEXADECANE(Non-covalent)

R16.11: 4 residues within 4Å: Chain A: L.367, I.371, I.375 Ligands: ZFC.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.367, A:I.371, A:I.371, A:I.375 R16.28: 4 residues within 4Å: Chain A: L.282, A.286 Chain B: L.859, Y.866 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.282, A:A.286 R16.39: 4 residues within 4Å: Chain A: L.859, Y.866 Chain B: L.282, A.286 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.282, B:A.286 R16.40: 4 residues within 4Å: Chain B: L.367, I.371, I.375 Ligands: ZFC.47 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.367, B:I.371, B:I.371, B:I.375

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

NAG.27: 3 residues within 4Å: Chain A: E.205, G.206, N.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.205 NAG.56: 3 residues within 4Å: Chain B: E.205, G.206, N.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.205

4 x PLM: PALMITIC ACID(Non-covalent)(Covalent)

PLM.62: 7 residues within 4Å: Chain A: I.755, I.758, I.759, Y.762 Chain D: C.44 Ligands: 3PE.4, ZFC.61 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.755, A:I.758, A:I.758, A:I.759, A:Y.762, A:Y.762 PLM.63: 5 residues within 4Å: Chain A: L.692, L.696 Chain D: I.39, C.43 Ligands: 3PE.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.692, A:L.696 PLM.69: 6 residues within 4Å: Chain B: I.755, I.758, I.759 Chain F: C.44 Ligands: 3PE.32, ZFC.68 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.755, B:I.758, B:I.759 PLM.70: 5 residues within 4Å: Chain B: L.692, L.696 Chain F: I.39, C.43 Ligands: 3PE.32 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.692, B:L.696

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeong, H. et al., Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature (2022)

Release Date

2022-10-19

Peptides

Transmembrane channel-like protein 1: AB
CALMyrin (Calcium and Integrin Binding protein) homolog: CE
Transmembrane inner ear expressed protein: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
E

D
D

F
F

Membrane

We predict this structure to be a membrane protein.
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Transmembrane channel-like protein 1

CALMyrin (Calcium and Integrin Binding protein) homolog

Transmembrane inner ear expressed protein

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