SMTL ID : 7lhf.1

Structure of full-length IP3R1 channel solubilized in LNMG & lipid in the apo-state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

28 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)(Covalent)

PLX.1: 12 residues within 4Å: Chain A: T.2299 Chain C: L.2526, M.2528 Chain D: F.2558, A.2559, V.2562, I.2563, L.2567, F.2570 Ligands: PLX.2, PLX.3, PLX.20 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.2559, D:V.2562, D:I.2563, D:L.2567, D:F.2570, D:F.2570 Salt bridges: D:E.2554 Hydrogen bonds: A:T.2299 PLX.2: 9 residues within 4Å: Chain A: G.2298, T.2299, L.2300 Chain D: F.2457, E.2554, P.2556, L.2557, A.2560 Ligands: PLX.1 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.2457 PLX.3: 12 residues within 4Å: Chain A: S.2273, F.2276, L.2284, A.2287, L.2412, R.2418 Chain C: I.2437, A.2440, I.2445, Y.2448 Ligands: PLX.1, PLX.18 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.2437, C:Y.2448, A:A.2287, A:L.2412 PLX.4: 6 residues within 4Å: Chain A: Y.2290, H.2404, F.2406, F.2407 Chain C: I.2452, V.2453 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.2452, C:V.2453, A:F.2407 Salt bridges: A:H.2404 PLX.5: 5 residues within 4Å: Chain A: G.2433, R.2434, I.2437 Ligands: PLX.7, PLX.12 No protein-ligand interaction detected (PLIP) PLX.6: 4 residues within 4Å: Chain A: E.2386, Y.2389, D.2414, Y.2417 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.2417, A:Y.2417 Salt bridges: A:E.2386 PLX.7: 8 residues within 4Å: Chain A: Y.2417, I.2426, K.2427, T.2430, R.2431 Chain C: L.2446, M.2571 Ligands: PLX.5 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.2446, A:Y.2417, A:K.2427, A:K.2427 Hydrogen bonds: A:T.2430 Salt bridges: A:K.2427 PLX.10: 11 residues within 4Å: Chain A: L.2526, M.2528 Chain B: T.2299 Chain C: F.2558, A.2559, V.2562, I.2563, L.2567, F.2570 Ligands: PLX.11, PLX.12 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.2559, C:V.2562, C:I.2563, C:L.2567, C:F.2570 Hydrogen bonds: B:T.2299 PLX.11: 9 residues within 4Å: Chain B: G.2298, T.2299, L.2300 Chain C: F.2457, E.2554, P.2556, L.2557, A.2560 Ligands: PLX.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.2457 PLX.12: 10 residues within 4Å: Chain A: I.2437, Y.2448 Chain B: S.2273, F.2276, L.2284, A.2287, L.2412, R.2418 Ligands: PLX.5, PLX.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.2287, B:L.2412, A:Y.2448 PLX.13: 6 residues within 4Å: Chain A: I.2452, V.2453 Chain B: Y.2290, H.2404, F.2406, F.2407 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.2452, A:V.2453, B:F.2407 Salt bridges: B:H.2404 PLX.14: 6 residues within 4Å: Chain B: T.2430, G.2433, R.2434, I.2437 Ligands: PLX.16, PLX.32 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.2430 PLX.15: 7 residues within 4Å: Chain B: E.2386, Y.2389, D.2414, Y.2417, R.2418, L.2423 Ligands: PLX.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.2417, B:Y.2417 Salt bridges: B:E.2386 PLX.16: 11 residues within 4Å: Chain A: L.2446, M.2571 Chain B: Y.2417, L.2423, I.2426, K.2427, T.2430, R.2431 Ligands: PLX.14, PLX.15, PLX.30 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.2417, B:L.2423, B:I.2426, B:K.2427, B:T.2430, A:L.2446 Hydrogen bonds: B:T.2430 Salt bridges: B:K.2427 PLX.17: 8 residues within 4Å: Chain C: Y.2290, H.2404, F.2406, F.2407 Chain D: L.2449, I.2452, V.2453, L.2456 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.2407, D:L.2449, D:I.2452, D:V.2453 Salt bridges: C:H.2404, C:H.2404, C:H.2404 PLX.18: 7 residues within 4Å: Chain C: T.2430, R.2431, G.2433, R.2434, I.2437 Ligands: PLX.3, PLX.20 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.2430 PLX.19: 6 residues within 4Å: Chain C: E.2386, Y.2389, D.2414, Y.2417, L.2423 Ligands: PLX.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.2417, C:Y.2417 Salt bridges: C:E.2386 PLX.20: 10 residues within 4Å: Chain C: F.2413, Y.2417, L.2423, I.2426, K.2427, T.2430, R.2431 Ligands: PLX.1, PLX.18, PLX.19 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.2413, C:Y.2417, C:Y.2417, C:L.2423, C:I.2426, C:K.2427, C:T.2430 Hydrogen bonds: C:T.2430 Salt bridges: C:K.2427 PLX.21: 12 residues within 4Å: Chain B: F.2558, A.2559, V.2562, I.2563, L.2567, F.2570 Chain C: T.2299 Chain D: L.2526, M.2528 Ligands: PLX.22, PLX.23, PLX.29 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.2559, B:V.2562, B:I.2563, B:L.2567, B:F.2570, B:F.2570 Hydrogen bonds: C:T.2299 PLX.22: 9 residues within 4Å: Chain B: F.2457, E.2554, P.2556, L.2557, A.2560 Chain C: G.2298, T.2299, L.2300 Ligands: PLX.21 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.2457 PLX.23: 10 residues within 4Å: Chain C: F.2276, L.2284, A.2287, L.2412, R.2418 Chain D: I.2437, I.2445, Y.2448 Ligands: PLX.21, PLX.27 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:A.2287, C:L.2412, D:I.2445, D:Y.2448 PLX.26: 6 residues within 4Å: Chain B: I.2452, V.2453 Chain D: Y.2290, H.2404, F.2406, F.2407 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.2407, B:I.2452, B:V.2453 Salt bridges: D:H.2404 PLX.27: 8 residues within 4Å: Chain B: F.2570 Chain D: T.2430, R.2431, G.2433, R.2434, I.2437 Ligands: PLX.23, PLX.29 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.2570, D:T.2430 PLX.28: 7 residues within 4Å: Chain D: E.2386, Y.2389, D.2414, Y.2417, R.2418, L.2423 Ligands: PLX.29 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.2417, D:Y.2417 Salt bridges: D:E.2386 PLX.29: 12 residues within 4Å: Chain B: L.2446, F.2570, M.2571 Chain D: Y.2417, L.2423, I.2426, K.2427, T.2430, R.2431 Ligands: PLX.21, PLX.27, PLX.28 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.2417, D:L.2423, D:I.2426, D:K.2427, D:T.2430, B:L.2446, B:F.2570 Hydrogen bonds: D:T.2430 Salt bridges: D:K.2427 PLX.30: 12 residues within 4Å: Chain A: F.2558, A.2559, V.2562, I.2563, L.2567, F.2570 Chain B: L.2526, M.2528 Chain D: T.2299 Ligands: PLX.16, PLX.31, PLX.32 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:T.2299 Hydrophobic interactions: A:A.2559, A:V.2562, A:I.2563, A:L.2567, A:F.2570 PLX.31: 9 residues within 4Å: Chain A: F.2457, E.2554, P.2556, L.2557, A.2560 Chain D: G.2298, T.2299, L.2300 Ligands: PLX.30 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.2457 PLX.32: 11 residues within 4Å: Chain B: I.2437, I.2445, Y.2448 Chain D: S.2273, F.2276, L.2284, A.2287, L.2412, R.2418 Ligands: PLX.14, PLX.30 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.2445, B:Y.2448, D:A.2287, D:L.2412

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: C.2606, C.2609, H.2626, H.2631 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.2606, A:H.2626, A:H.2631 ZN.9: 4 residues within 4Å: Chain B: C.2606, C.2609, H.2626, H.2631 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.2606, B:H.2626, B:H.2631 ZN.24: 4 residues within 4Å: Chain C: C.2606, C.2609, H.2626, H.2631 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.2606, C:H.2626, C:H.2631 ZN.25: 4 residues within 4Å: Chain D: C.2606, C.2609, H.2626, H.2631 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.2606, D:H.2626, D:H.2631

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baker, M.R. et al., Cryo-EM structure of type 1 IP3R channel in a lipid bilayer. Commun Biol (2021)

Release Date

2021-06-02

Peptides

Inositol 1,4,5-trisphosphate receptor type 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
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Inositol 1,4,5-trisphosphate receptor type 1