SMTL ID : 9heo.1

Open-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4948, A:C.4951, A:H.4968, A:H.4973 ZN.26: 4 residues within 4Å: Chain C: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4948, C:C.4951, C:H.4968, C:H.4973 ZN.48: 4 residues within 4Å: Chain G: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4948, G:C.4951, G:H.4968, G:H.4973 ZN.74: 4 residues within 4Å: Chain J: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4948, J:C.4951, J:H.4968, J:H.4973

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 14 residues within 4Å: Chain A: K.4201, K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.4949, A:I.4950, A:H.4973, A:N.4974, A:L.4975 Salt bridges: A:K.4204, A:K.4204, A:K.4204, A:R.4205 ATP.27: 14 residues within 4Å: Chain C: K.4201, K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:F.4949, C:I.4950, C:H.4973, C:N.4974, C:L.4975 Salt bridges: C:K.4204, C:K.4204, C:R.4205 ATP.49: 14 residues within 4Å: Chain G: K.4201, K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:F.4949, G:I.4950, G:H.4973, G:N.4974, G:L.4975 Salt bridges: G:K.4204, G:K.4204, G:K.4204, G:R.4205 ATP.75: 14 residues within 4Å: Chain J: K.4201, K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:K.4201, J:F.4949, J:I.4950, J:H.4973, J:N.4974, J:L.4975 Salt bridges: J:K.4204, J:K.4204, J:K.4204, J:R.4205

4 x CFF: CAFFEINE(Non-covalent)

CFF.3: 8 residues within 4Å: Chain A: F.3743, E.4229, I.4232, Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.4236, A:Y.5004 pi-Stacking: A:W.4706, A:W.4706, A:W.4706 CFF.28: 8 residues within 4Å: Chain C: F.3743, E.4229, I.4232, Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.4236, C:Y.5004 pi-Stacking: C:W.4706, C:W.4706, C:W.4706 CFF.50: 8 residues within 4Å: Chain G: F.3743, E.4229, I.4232, Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Q.4236, G:Y.5004 pi-Stacking: G:W.4706, G:W.4706, G:W.4706 CFF.76: 8 residues within 4Å: Chain J: F.3743, E.4229, I.4232, Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:Q.4236, J:Y.5004 pi-Stacking: J:W.4706, J:W.4706, J:W.4706

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.3883, E.3957, T.4991 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.3883, A:E.3957, A:E.3957, A:T.4991 CA.29: 3 residues within 4Å: Chain C: E.3883, E.3957, T.4991 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.3883, C:E.3957, C:E.3957, C:T.4991 CA.51: 3 residues within 4Å: Chain G: E.3883, E.3957, T.4991 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3883, G:E.3957, G:E.3957, G:T.4991 CA.77: 3 residues within 4Å: Chain J: E.3883, E.3957, T.4991 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.3883, J:E.3957, J:E.3957, J:T.4991

72 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.5: 7 residues within 4Å: Chain A: T.4641, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.6 Ligand excluded by PLIP POV.6: 18 residues within 4Å: Chain A: L.4780, W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801 Chain J: L.4840, V.4843, V.4844, N.4847, F.4848 Ligands: POV.5, POV.12, POV.67, POV.68 Ligand excluded by PLIP POV.7: 17 residues within 4Å: Chain A: V.4828, V.4831, G.4832, A.4835, M.4870, T.4871, Y.4873, L.4874, M.4877 Chain J: E.4900, L.4901 Ligands: POV.8, POV.23, POV.24, POV.25, POV.69, POV.70 Ligand excluded by PLIP POV.8: 14 residues within 4Å: Chain A: T.4821, H.4822, G.4824, K.4825, V.4828, V.4831, M.4877 Chain J: I.4908, F.4912 Ligands: POV.7, POV.9, POV.10, POV.69, POV.70 Ligand excluded by PLIP POV.9: 5 residues within 4Å: Chain A: T.4821 Ligands: POV.8, POV.10, POV.11, POV.13 Ligand excluded by PLIP POV.10: 11 residues within 4Å: Chain A: R.4814, L.4817, S.4818, V.4820, T.4821 Chain J: F.4913 Ligands: POV.8, POV.9, POV.11, POV.12, POV.68 Ligand excluded by PLIP POV.11: 7 residues within 4Å: Chain A: N.4777 Ligands: POV.9, POV.10, POV.12, POV.13, POV.67, POV.68 Ligand excluded by PLIP POV.12: 12 residues within 4Å: Chain A: N.4777, S.4778, Y.4781, W.4784, F.4798, M.4808 Ligands: POV.6, POV.10, POV.11, POV.13, POV.67, POV.68 Ligand excluded by PLIP POV.13: 6 residues within 4Å: Chain A: N.4777, L.4780 Ligands: POV.9, POV.11, POV.12, POV.14 Ligand excluded by PLIP POV.14: 7 residues within 4Å: Chain A: K.4688, F.4774, T.4775, N.4777, L.4780 Ligands: POV.13, POV.15 Ligand excluded by PLIP POV.15: 9 residues within 4Å: Chain A: R.4663, D.4685, V.4687, K.4688, W.4691, F.4770, G.4771, T.4775 Ligands: POV.14 Ligand excluded by PLIP POV.16: 15 residues within 4Å: Chain A: L.4840, V.4844, N.4847, F.4848, F.4849, Y.4899, F.4906, T.4909 Chain C: Y.4620, L.4804 Ligands: POV.17, POV.31, POV.35, POV.36, POV.37 Ligand excluded by PLIP POV.17: 12 residues within 4Å: Chain A: Y.4899, Y.4902, V.4905, T.4909, F.4913 Ligands: POV.16, POV.18, POV.19, POV.31, POV.34, POV.36, POV.37 Ligand excluded by PLIP POV.18: 5 residues within 4Å: Chain A: Y.4902 Ligands: POV.17, POV.19, POV.32, POV.33 Ligand excluded by PLIP POV.19: 11 residues within 4Å: Chain A: G.4896, D.4897, E.4898, E.4900, L.4901, Y.4902, V.4905 Ligands: POV.17, POV.18, POV.32, POV.33 Ligand excluded by PLIP POV.20: 13 residues within 4Å: Chain A: F.4565, L.4568, F.4569, Y.4570, K.4571, E.4623, E.4624 Chain J: D.4868, M.4869, M.4870 Ligands: POV.21, POV.22, POV.80 Ligand excluded by PLIP POV.21: 13 residues within 4Å: Chain A: F.4554, L.4557, F.4558, F.4561, A.4562, F.4565, M.4629, G.4809, V.4810, K.4811 Ligands: POV.20, POV.22, POV.80 Ligand excluded by PLIP POV.22: 13 residues within 4Å: Chain A: N.4564, F.4565, L.4568, L.4803 Chain J: M.4829, G.4832, A.4835, V.4836, Y.4839, Y.4873 Ligands: POV.20, POV.21, POV.80 Ligand excluded by PLIP POV.23: 13 residues within 4Å: Chain A: D.4868, M.4869, M.4870 Chain C: F.4565, L.4568, F.4569, Y.4570, K.4571, E.4623, E.4624 Ligands: POV.7, POV.24, POV.25 Ligand excluded by PLIP POV.24: 13 residues within 4Å: Chain C: F.4554, L.4557, F.4558, F.4561, A.4562, F.4565, M.4629, G.4809, V.4810, K.4811 Ligands: POV.7, POV.23, POV.25 Ligand excluded by PLIP POV.25: 13 residues within 4Å: Chain A: M.4829, G.4832, A.4835, V.4836, Y.4839, Y.4873 Chain C: N.4564, F.4565, L.4568, L.4803 Ligands: POV.7, POV.23, POV.24 Ligand excluded by PLIP POV.30: 7 residues within 4Å: Chain C: T.4641, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.31 Ligand excluded by PLIP POV.31: 18 residues within 4Å: Chain A: L.4840, V.4843, V.4844, N.4847, F.4848 Chain C: L.4780, W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801 Ligands: POV.16, POV.17, POV.30, POV.37 Ligand excluded by PLIP POV.32: 17 residues within 4Å: Chain A: E.4900, L.4901 Chain C: V.4828, V.4831, G.4832, A.4835, M.4870, T.4871, Y.4873, L.4874, M.4877 Ligands: POV.18, POV.19, POV.33, POV.45, POV.46, POV.47 Ligand excluded by PLIP POV.33: 13 residues within 4Å: Chain A: I.4908, F.4912 Chain C: T.4821, H.4822, G.4824, K.4825, V.4828, V.4831, M.4877 Ligands: POV.18, POV.19, POV.32, POV.34 Ligand excluded by PLIP POV.34: 6 residues within 4Å: Chain C: T.4821 Ligands: POV.17, POV.33, POV.35, POV.36, POV.38 Ligand excluded by PLIP POV.35: 11 residues within 4Å: Chain A: F.4913 Chain C: M.4808, R.4814, L.4817, S.4818, V.4820, T.4821 Ligands: POV.16, POV.34, POV.36, POV.37 Ligand excluded by PLIP POV.36: 7 residues within 4Å: Chain C: N.4777 Ligands: POV.16, POV.17, POV.34, POV.35, POV.37, POV.38 Ligand excluded by PLIP POV.37: 12 residues within 4Å: Chain C: N.4777, S.4778, Y.4781, W.4784, F.4798, M.4808 Ligands: POV.16, POV.17, POV.31, POV.35, POV.36, POV.38 Ligand excluded by PLIP POV.38: 6 residues within 4Å: Chain C: N.4777, L.4780 Ligands: POV.34, POV.36, POV.37, POV.39 Ligand excluded by PLIP POV.39: 7 residues within 4Å: Chain C: K.4688, F.4774, T.4775, N.4777, L.4780 Ligands: POV.38, POV.40 Ligand excluded by PLIP POV.40: 9 residues within 4Å: Chain C: R.4663, D.4685, V.4687, K.4688, W.4691, F.4770, G.4771, T.4775 Ligands: POV.39 Ligand excluded by PLIP POV.41: 15 residues within 4Å: Chain C: L.4840, V.4844, N.4847, F.4848, F.4849, Y.4899, F.4906, T.4909 Chain G: Y.4620, L.4804 Ligands: POV.42, POV.53, POV.57, POV.58, POV.59 Ligand excluded by PLIP POV.42: 11 residues within 4Å: Chain C: Y.4899, Y.4902, V.4905, T.4909 Ligands: POV.41, POV.43, POV.44, POV.53, POV.56, POV.58, POV.59 Ligand excluded by PLIP POV.43: 5 residues within 4Å: Chain C: Y.4902 Ligands: POV.42, POV.44, POV.54, POV.55 Ligand excluded by PLIP POV.44: 11 residues within 4Å: Chain C: G.4896, D.4897, E.4898, E.4900, L.4901, Y.4902, V.4905 Ligands: POV.42, POV.43, POV.54, POV.55 Ligand excluded by PLIP POV.45: 13 residues within 4Å: Chain C: D.4868, M.4869, M.4870 Chain G: F.4565, L.4568, F.4569, Y.4570, K.4571, E.4623, E.4624 Ligands: POV.32, POV.46, POV.47 Ligand excluded by PLIP POV.46: 13 residues within 4Å: Chain G: F.4554, L.4557, F.4558, F.4561, A.4562, F.4565, M.4629, G.4809, V.4810, K.4811 Ligands: POV.32, POV.45, POV.47 Ligand excluded by PLIP POV.47: 13 residues within 4Å: Chain C: M.4829, G.4832, A.4835, V.4836, Y.4839, Y.4873 Chain G: N.4564, F.4565, L.4568, L.4803 Ligands: POV.32, POV.45, POV.46 Ligand excluded by PLIP POV.52: 7 residues within 4Å: Chain G: T.4641, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.53 Ligand excluded by PLIP POV.53: 18 residues within 4Å: Chain C: L.4840, V.4843, V.4844, N.4847, F.4848 Chain G: L.4780, W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801 Ligands: POV.41, POV.42, POV.52, POV.59 Ligand excluded by PLIP POV.54: 17 residues within 4Å: Chain C: E.4900, L.4901 Chain G: V.4828, V.4831, G.4832, A.4835, M.4870, T.4871, Y.4873, L.4874, M.4877 Ligands: POV.43, POV.44, POV.55, POV.71, POV.72, POV.73 Ligand excluded by PLIP POV.55: 13 residues within 4Å: Chain C: I.4908, F.4912 Chain G: T.4821, H.4822, G.4824, K.4825, V.4828, V.4831, M.4877 Ligands: POV.43, POV.44, POV.54, POV.56 Ligand excluded by PLIP POV.56: 6 residues within 4Å: Chain G: T.4821 Ligands: POV.42, POV.55, POV.57, POV.58, POV.60 Ligand excluded by PLIP POV.57: 9 residues within 4Å: Chain C: F.4913 Chain G: R.4814, L.4817, S.4818, T.4821 Ligands: POV.41, POV.56, POV.58, POV.59 Ligand excluded by PLIP POV.58: 7 residues within 4Å: Chain G: N.4777 Ligands: POV.41, POV.42, POV.56, POV.57, POV.59, POV.60 Ligand excluded by PLIP POV.59: 12 residues within 4Å: Chain G: N.4777, S.4778, Y.4781, W.4784, F.4798, M.4808 Ligands: POV.41, POV.42, POV.53, POV.57, POV.58, POV.60 Ligand excluded by PLIP POV.60: 6 residues within 4Å: Chain G: N.4777, L.4780 Ligands: POV.56, POV.58, POV.59, POV.61 Ligand excluded by PLIP POV.61: 7 residues within 4Å: Chain G: K.4688, F.4774, T.4775, N.4777, L.4780 Ligands: POV.60, POV.62 Ligand excluded by PLIP POV.62: 9 residues within 4Å: Chain G: R.4663, D.4685, V.4687, K.4688, W.4691, F.4770, G.4771, T.4775 Ligands: POV.61 Ligand excluded by PLIP POV.63: 15 residues within 4Å: Chain G: L.4840, V.4844, N.4847, F.4848, F.4849, Y.4899, F.4906, T.4909 Chain J: Y.4620, L.4804 Ligands: POV.64, POV.79, POV.83, POV.84, POV.85 Ligand excluded by PLIP POV.64: 10 residues within 4Å: Chain G: Y.4902, T.4909, F.4913 Ligands: POV.63, POV.65, POV.66, POV.79, POV.83, POV.84, POV.85 Ligand excluded by PLIP POV.65: 5 residues within 4Å: Chain G: Y.4902 Ligands: POV.64, POV.66, POV.80, POV.81 Ligand excluded by PLIP POV.66: 11 residues within 4Å: Chain G: G.4896, D.4897, E.4898, E.4900, L.4901, Y.4902, V.4905 Ligands: POV.64, POV.65, POV.80, POV.81 Ligand excluded by PLIP POV.67: 14 residues within 4Å: Chain A: Y.4620, L.4804 Chain J: L.4840, V.4844, N.4847, F.4848, F.4849, Y.4899, F.4906, T.4909 Ligands: POV.6, POV.11, POV.12, POV.68 Ligand excluded by PLIP POV.68: 11 residues within 4Å: Chain J: Y.4899, Y.4902, T.4909, F.4913 Ligands: POV.6, POV.10, POV.11, POV.12, POV.67, POV.69, POV.70 Ligand excluded by PLIP POV.69: 5 residues within 4Å: Chain J: Y.4902 Ligands: POV.7, POV.8, POV.68, POV.70 Ligand excluded by PLIP POV.70: 11 residues within 4Å: Chain J: G.4896, D.4897, E.4898, E.4900, L.4901, Y.4902, V.4905 Ligands: POV.7, POV.8, POV.68, POV.69 Ligand excluded by PLIP POV.71: 13 residues within 4Å: Chain G: D.4868, M.4869, M.4870 Chain J: F.4565, L.4568, F.4569, Y.4570, K.4571, E.4623, E.4624 Ligands: POV.54, POV.72, POV.73 Ligand excluded by PLIP POV.72: 13 residues within 4Å: Chain J: F.4554, L.4557, F.4558, F.4561, A.4562, F.4565, M.4629, G.4809, V.4810, K.4811 Ligands: POV.54, POV.71, POV.73 Ligand excluded by PLIP POV.73: 13 residues within 4Å: Chain G: M.4829, G.4832, A.4835, V.4836, Y.4839, Y.4873 Chain J: N.4564, F.4565, L.4568, L.4803 Ligands: POV.54, POV.71, POV.72 Ligand excluded by PLIP POV.78: 7 residues within 4Å: Chain J: T.4641, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.79 Ligand excluded by PLIP POV.79: 18 residues within 4Å: Chain G: L.4840, V.4843, V.4844, N.4847, F.4848 Chain J: L.4780, W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801 Ligands: POV.63, POV.64, POV.78, POV.85 Ligand excluded by PLIP POV.80: 17 residues within 4Å: Chain G: E.4900, L.4901 Chain J: V.4828, V.4831, G.4832, A.4835, M.4870, T.4871, Y.4873, L.4874, M.4877 Ligands: POV.20, POV.21, POV.22, POV.65, POV.66, POV.81 Ligand excluded by PLIP POV.81: 13 residues within 4Å: Chain G: I.4908, F.4912 Chain J: T.4821, H.4822, G.4824, K.4825, V.4828, V.4831, M.4877 Ligands: POV.65, POV.66, POV.80, POV.82 Ligand excluded by PLIP POV.82: 5 residues within 4Å: Chain J: T.4821 Ligands: POV.81, POV.83, POV.84, POV.86 Ligand excluded by PLIP POV.83: 12 residues within 4Å: Chain G: F.4913 Chain J: M.4808, R.4814, L.4817, S.4818, V.4820, T.4821 Ligands: POV.63, POV.64, POV.82, POV.84, POV.85 Ligand excluded by PLIP POV.84: 7 residues within 4Å: Chain J: N.4777 Ligands: POV.63, POV.64, POV.82, POV.83, POV.85, POV.86 Ligand excluded by PLIP POV.85: 12 residues within 4Å: Chain J: N.4777, S.4778, Y.4781, W.4784, F.4798, M.4808 Ligands: POV.63, POV.64, POV.79, POV.83, POV.84, POV.86 Ligand excluded by PLIP POV.86: 6 residues within 4Å: Chain J: N.4777, L.4780 Ligands: POV.82, POV.84, POV.85, POV.87 Ligand excluded by PLIP POV.87: 7 residues within 4Å: Chain J: K.4688, F.4774, T.4775, N.4777, L.4780 Ligands: POV.86, POV.88 Ligand excluded by PLIP POV.88: 9 residues within 4Å: Chain J: R.4663, D.4685, V.4687, K.4688, W.4691, F.4770, G.4771, T.4775 Ligands: POV.87 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C. et al., Open-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP. To Be Published

Release Date

2025-09-17

Peptides

Ryanodine receptor 1: ACGJ
Nanobody 9657: BDHK
Peptidyl-prolyl cis-trans isomerase FKBP1B: EFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

G
G

J
J

B
B

D
D

H
H

K
K

E
E

F
F

I
I

L
L

Membrane

We predict this structure to be a membrane protein.
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Ryanodine receptor 1

Nanobody 9657

Peptidyl-prolyl cis-trans isomerase FKBP1B

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