SMTL ID : 9heq.1

Open-state RyR1 in 0.01% POPC micelles, in complex with a nanobody and FKBP12

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

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

POV.1: 10 residues within 4Å: Chain A: F.4561, F.4565, L.4803 Chain C: M.4829, G.4832, A.4835, V.4836, Y.4839, Y.4873 Ligands: POV.45 Ligand excluded by PLIP POV.5: 10 residues within 4Å: Chain A: W.4634, L.4638, T.4641, L.4642, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.6 Ligand excluded by PLIP POV.6: 15 residues within 4Å: Chain A: L.4780, W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801 Chain C: N.4847, F.4848 Ligands: POV.5, POV.7, POV.11, POV.27 Ligand excluded by PLIP POV.7: 12 residues within 4Å: Chain A: Y.4620 Chain C: L.4840, Y.4841, V.4844, N.4847, F.4848, F.4849, Y.4899, Y.4902 Ligands: POV.6, POV.11, POV.27 Ligand excluded by PLIP POV.8: 10 residues within 4Å: Chain A: M.4829, G.4832, V.4836, Y.4839, Y.4873 Chain G: F.4561, F.4565, L.4568, L.4803 Ligands: POV.28 Ligand excluded by PLIP POV.9: 12 residues within 4Å: Chain A: T.4821, H.4822, N.4823, G.4824, K.4825, V.4828, L.4834, M.4877, V.4881 Chain C: I.4908, F.4912 Ligands: POV.10 Ligand excluded by PLIP POV.10: 5 residues within 4Å: Chain A: T.4821, K.4825 Chain C: F.4913 Ligands: POV.9, POV.11 Ligand excluded by PLIP POV.11: 11 residues within 4Å: Chain A: N.4777, S.4778, L.4780, Y.4781, W.4784, F.4798, M.4808 Ligands: POV.6, POV.7, POV.10, POV.27 Ligand excluded by PLIP POV.12: 9 residues within 4Å: Chain A: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, F.4770, G.4771, T.4775 Ligand excluded by PLIP POV.14: 12 residues within 4Å: Chain A: L.4840, Y.4841, V.4844, N.4847, F.4848, F.4849, Y.4899, Y.4902 Chain G: Y.4620 Ligands: POV.15, POV.33, POV.37 Ligand excluded by PLIP POV.15: 7 residues within 4Å: Chain A: Y.4899, Y.4902, V.4905, T.4909 Ligands: POV.14, POV.33, POV.37 Ligand excluded by PLIP POV.16: 8 residues within 4Å: Chain A: L.4901 Chain G: V.4828, V.4831, A.4835, M.4870, Y.4873, M.4877 Ligands: POV.34 Ligand excluded by PLIP POV.20: 10 residues within 4Å: Chain C: W.4634, L.4638, T.4641, L.4642, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.21 Ligand excluded by PLIP POV.21: 14 residues within 4Å: Chain C: L.4780, W.4784, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801 Chain J: N.4847, F.4848 Ligands: POV.20, POV.24, POV.43, POV.44 Ligand excluded by PLIP POV.22: 13 residues within 4Å: Chain C: V.4820, T.4821, H.4822, G.4824, K.4825, V.4828, L.4834, M.4877, V.4881, L.4919 Chain J: I.4908, F.4912 Ligands: POV.23 Ligand excluded by PLIP POV.23: 5 residues within 4Å: Chain C: T.4821, K.4825 Chain J: F.4913 Ligands: POV.22, POV.24 Ligand excluded by PLIP POV.24: 10 residues within 4Å: Chain C: N.4777, S.4778, L.4780, Y.4781, W.4784, M.4808 Ligands: POV.21, POV.23, POV.43, POV.44 Ligand excluded by PLIP POV.25: 10 residues within 4Å: Chain C: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, I.4767, F.4770, G.4771, T.4775 Ligand excluded by PLIP POV.27: 7 residues within 4Å: Chain C: Y.4899, Y.4902, V.4905, T.4909 Ligands: POV.6, POV.7, POV.11 Ligand excluded by PLIP POV.28: 8 residues within 4Å: Chain A: V.4828, V.4831, A.4835, M.4870, Y.4873, M.4877 Chain C: L.4901 Ligands: POV.8 Ligand excluded by PLIP POV.32: 10 residues within 4Å: Chain G: W.4634, L.4638, T.4641, L.4642, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.33 Ligand excluded by PLIP POV.33: 15 residues within 4Å: Chain A: 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.14, POV.15, POV.32, POV.37 Ligand excluded by PLIP POV.34: 10 residues within 4Å: Chain G: M.4829, G.4832, V.4836, Y.4839, Y.4873 Chain J: F.4561, F.4565, L.4568, L.4803 Ligands: POV.16 Ligand excluded by PLIP POV.35: 12 residues within 4Å: Chain A: I.4908, F.4912 Chain G: T.4821, H.4822, N.4823, G.4824, K.4825, V.4828, L.4834, M.4877, V.4881 Ligands: POV.36 Ligand excluded by PLIP POV.36: 5 residues within 4Å: Chain A: F.4913 Chain G: T.4821, K.4825 Ligands: POV.35, POV.37 Ligand excluded by PLIP POV.37: 11 residues within 4Å: Chain G: N.4777, S.4778, L.4780, Y.4781, W.4784, F.4798, M.4808 Ligands: POV.14, POV.15, POV.33, POV.36 Ligand excluded by PLIP POV.38: 9 residues within 4Å: Chain G: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, F.4770, G.4771, T.4775 Ligand excluded by PLIP POV.40: 12 residues within 4Å: Chain G: L.4840, Y.4841, V.4844, N.4847, F.4848, F.4849, Y.4899, Y.4902 Chain J: Y.4620 Ligands: POV.41, POV.50, POV.54 Ligand excluded by PLIP POV.41: 7 residues within 4Å: Chain G: Y.4899, Y.4902, V.4905, T.4909 Ligands: POV.40, POV.50, POV.54 Ligand excluded by PLIP POV.42: 8 residues within 4Å: Chain G: L.4901 Chain J: V.4828, V.4831, A.4835, M.4870, Y.4873, M.4877 Ligands: POV.51 Ligand excluded by PLIP POV.43: 12 residues within 4Å: Chain C: Y.4620 Chain J: L.4840, Y.4841, V.4844, N.4847, F.4848, F.4849, Y.4899, Y.4902 Ligands: POV.21, POV.24, POV.44 Ligand excluded by PLIP POV.44: 7 residues within 4Å: Chain J: Y.4899, Y.4902, V.4905, T.4909 Ligands: POV.21, POV.24, POV.43 Ligand excluded by PLIP POV.45: 10 residues within 4Å: Chain C: V.4828, V.4831, G.4832, A.4835, M.4870, Y.4873, L.4874, M.4877 Chain J: L.4901 Ligands: POV.1 Ligand excluded by PLIP POV.49: 10 residues within 4Å: Chain J: W.4634, L.4638, T.4641, L.4642, F.4645, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.50 Ligand excluded by PLIP POV.50: 15 residues within 4Å: Chain G: 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.40, POV.41, POV.49, POV.54 Ligand excluded by PLIP POV.51: 11 residues within 4Å: Chain C: F.4561, N.4564, F.4565, L.4568, L.4803 Chain J: M.4829, G.4832, V.4836, Y.4839, Y.4873 Ligands: POV.42 Ligand excluded by PLIP POV.52: 12 residues within 4Å: Chain G: I.4908, F.4912 Chain J: T.4821, H.4822, N.4823, G.4824, K.4825, V.4828, L.4834, M.4877, V.4881 Ligands: POV.53 Ligand excluded by PLIP POV.53: 5 residues within 4Å: Chain G: F.4913 Chain J: T.4821, K.4825 Ligands: POV.52, POV.54 Ligand excluded by PLIP POV.54: 11 residues within 4Å: Chain J: N.4777, S.4778, L.4780, Y.4781, W.4784, F.4798, M.4808 Ligands: POV.40, POV.41, POV.50, POV.53 Ligand excluded by PLIP POV.55: 9 residues within 4Å: Chain J: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, F.4770, G.4771, T.4775 Ligand excluded by PLIP

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

ATP.2: 12 residues within 4Å: Chain A: K.4201, K.4204, R.4205, M.4944, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, L.4975 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.4201, A:F.4949, A:I.4950, A:T.4969, A:H.4973, A:L.4975 Salt bridges: A:K.4201, A:K.4204, A:K.4204, A:R.4205 ATP.17: 13 residues within 4Å: Chain C: K.4201, K.4204, R.4205, M.4944, 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 C Hydrogen bonds: C:F.4949, C:I.4950, C:T.4969, C:H.4973, C:L.4975 Salt bridges: C:K.4201, C:K.4204, C:K.4204, C:R.4205 ATP.29: 12 residues within 4Å: Chain G: K.4201, K.4204, R.4205, M.4944, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, L.4975 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:K.4201, G:F.4949, G:I.4950, G:T.4969, G:H.4973, G:L.4975 Salt bridges: G:K.4201, G:K.4204, G:K.4204, G:R.4205 ATP.46: 12 residues within 4Å: Chain J: K.4201, K.4204, R.4205, M.4944, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, L.4975 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:K.4201, J:F.4949, J:I.4950, J:T.4969, J:H.4973, J:L.4975 Salt bridges: J:K.4201, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.4236, A:Y.5004 pi-Stacking: A:W.4706 CFF.18: 7 residues within 4Å: Chain C: F.3743, E.4229, Q.4236, W.4706, I.4986, W.5001, Y.5004 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.4236, C:Y.5004 pi-Stacking: C:W.4706 CFF.30: 8 residues within 4Å: Chain G: F.3743, E.4229, I.4232, Q.4236, W.4706, I.4986, W.5001, Y.5004 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Q.4236, G:Y.5004 pi-Stacking: G:W.4706 CFF.47: 8 residues within 4Å: Chain J: F.3743, E.4229, I.4232, Q.4236, W.4706, I.4986, W.5001, Y.5004 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Q.4236, J:Y.5004 pi-Stacking: J:W.4706

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.3957, T.4991, E.4992 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3957, A:E.3957, A:T.4991 CA.19: 3 residues within 4Å: Chain C: E.3957, T.4991, E.4992 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.3957, C:E.3957, C:T.4991 CA.31: 3 residues within 4Å: Chain G: E.3957, T.4991, E.4992 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3957, G:E.3957, G:T.4991 CA.48: 3 residues within 4Å: Chain J: E.3957, T.4991, E.4992 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.3957, J:E.3957, J:T.4991

4 x ZN: ZINC ION(Non-covalent)

ZN.13: 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.39: 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.56: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C. et al., Open-state RyR1 in 0.01% 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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