SMTL ID : 6pw4.1

Cryo-EM Structure of Thermo-Sensitive TRP Channel TRP1 from the Alga Chlamydomonas reinhardtii in Detergent

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Covalent)

PIO.1: 13 residues within 4Å: Chain A: V.437, T.438, T.441, K.442, W.502, L.503, I.510, F.621, L.623, S.624, S.625, F.758, K.762 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.503, A:I.510 Hydrogen bonds: A:T.438 Salt bridges: A:K.442, A:K.762, A:K.762 PIO.6: 14 residues within 4Å: Chain C: W.432, V.437, T.438, T.441, K.442, W.502, L.503, I.510, F.621, L.623, S.624, S.625, F.758, K.762 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.503, C:I.510 Hydrogen bonds: C:T.438 Salt bridges: C:K.442, C:K.762, C:K.762

2 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Covalent)

PCW.2: 22 residues within 4Å: Chain A: Y.440, W.449, G.450, L.454, A.457, W.461, F.481, D.490, S.491, R.492, P.494, W.495, Y.500, L.503, L.504, F.774 Chain D: Y.85, Y.87, Y.92, Y.95, W.125, Y.136 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.454, A:A.457, A:F.481, A:P.494, A:W.495, A:W.495, A:Y.500, A:Y.500, A:Y.500, A:Y.500, A:L.503, A:L.504, A:F.774 Hydrogen bonds: A:Y.440, A:Y.440, A:S.491, D:Y.87 Salt bridges: D:K.128 pi-Cation interactions: D:Y.85 PCW.7: 22 residues within 4Å: Chain B: Y.85, Y.87, Y.92, Y.95, W.125, Y.136 Chain C: Y.440, W.449, G.450, L.454, A.457, W.461, F.481, D.490, S.491, R.492, P.494, W.495, Y.500, L.503, L.504, F.774 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.454, C:A.457, C:F.481, C:P.494, C:W.495, C:W.495, C:Y.500, C:Y.500, C:Y.500, C:Y.500, C:L.503, C:L.504, C:F.774 Hydrogen bonds: C:Y.440, C:Y.440, C:S.491, B:Y.87 Salt bridges: B:K.128 pi-Cation interactions: B:Y.85

2 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Covalent)

CPL.3: 7 residues within 4Å: Chain A: Y.85, Y.87, Y.95, W.125, Y.136 Chain B: Y.440, Y.500 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B pi-Cation interactions: A:Y.85 Hydrophobic interactions: B:Y.440 Hydrogen bonds: B:Y.500 CPL.8: 7 residues within 4Å: Chain C: Y.85, Y.87, Y.95, W.125, Y.136 Chain D: Y.440, Y.500 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D pi-Cation interactions: C:Y.85 Hydrophobic interactions: D:Y.440 Hydrogen bonds: D:Y.500

4 x PIK: (2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate(Non-covalent)(Covalent)

PIK.4: 11 residues within 4Å: Chain B: V.437, T.438, T.441, K.442, L.499, F.621, L.623, S.624, S.625, A.626, I.627 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.441, B:F.621, B:A.626, B:I.627 Hydrogen bonds: B:T.438, B:T.438, B:T.441, B:S.625 Salt bridges: B:K.442, B:K.442, B:K.762 PIK.5: 15 residues within 4Å: Chain A: F.723, F.727, V.730 Chain B: M.564, S.565, G.567, W.568, V.570, D.604, L.611, M.612, M.634, K.635, L.638, I.639 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.568, B:L.611, B:M.634, B:L.638, B:L.638, A:F.723, A:F.727 Hydrogen bonds: B:K.635, B:K.635 PIK.9: 12 residues within 4Å: Chain D: V.437, T.438, T.441, K.442, L.499, L.503, F.621, L.623, S.624, S.625, A.626, I.627 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:T.441, D:L.503, D:F.621, D:A.626, D:I.627 Hydrogen bonds: D:T.438, D:T.438, D:T.441, D:S.625 Salt bridges: D:K.442, D:K.442, D:K.762 PIK.10: 15 residues within 4Å: Chain C: F.723, F.727, V.730 Chain D: M.564, S.565, G.567, W.568, V.570, D.604, L.611, M.612, M.634, K.635, L.638, I.639 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.568, D:L.611, D:M.634, D:L.638, D:L.638, C:F.723, C:F.727 Hydrogen bonds: D:K.635, D:K.635

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGoldrick, L.L. et al., Structure of the thermo-sensitive TRP channel TRP1 from the alga Chlamydomonas reinhardtii. Nat Commun (2019)

Release Date

2019-09-25

Peptides

TRP-like ion channel: 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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TRP-like ion channel

Related Entries With Identical Sequence