SMTL ID : 9r8o.1

Primed-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 ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 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:L.4975 Salt bridges: C:K.4201, C:K.4201, C:K.4204, C:R.4205, C:R.4205, C:R.4205 ATP.16: 13 residues within 4Å: Chain F: 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 F Hydrogen bonds: F:F.4949, F:I.4950, F:L.4975 Salt bridges: F:K.4201, F:K.4201, F:K.4204, F:R.4205, F:R.4205, F:R.4205 ATP.31: 13 residues within 4Å: Chain I: 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 I Hydrogen bonds: I:F.4949, I:I.4950, I:L.4975 Salt bridges: I:K.4201, I:K.4201, I:K.4204, I:R.4205, I:R.4205, I:R.4205 ATP.48: 13 residues within 4Å: Chain L: 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 L Hydrogen bonds: L:F.4949, L:I.4950, L:L.4975 Salt bridges: L:K.4201, L:K.4201, L:K.4204, L:R.4205, L:R.4205, L:R.4205

4 x CFF: CAFFEINE(Non-covalent)

CFF.2: 5 residues within 4Å: Chain C: F.3743, E.4229, W.4706, I.4986, W.5001 3 PLIP interactions: 3 interactions with chain C pi-Stacking: C:W.4706, C:W.4706, C:W.4706 CFF.17: 5 residues within 4Å: Chain F: F.3743, E.4229, W.4706, I.4986, W.5001 3 PLIP interactions: 3 interactions with chain F pi-Stacking: F:W.4706, F:W.4706, F:W.4706 CFF.32: 5 residues within 4Å: Chain I: F.3743, E.4229, W.4706, I.4986, W.5001 3 PLIP interactions: 3 interactions with chain I pi-Stacking: I:W.4706, I:W.4706, I:W.4706 CFF.49: 5 residues within 4Å: Chain L: F.3743, E.4229, W.4706, I.4986, W.5001 3 PLIP interactions: 3 interactions with chain L pi-Stacking: L:W.4706, L:W.4706, L:W.4706

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain C: H.3885, E.3957, Q.3960, T.4991, H.4993 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.3957, C:E.3957, C:T.4991 CA.18: 5 residues within 4Å: Chain F: H.3885, E.3957, Q.3960, T.4991, H.4993 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3957, F:E.3957, F:T.4991 CA.33: 5 residues within 4Å: Chain I: H.3885, E.3957, Q.3960, T.4991, H.4993 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.3957, I:E.3957, I:T.4991 CA.50: 5 residues within 4Å: Chain L: H.3885, E.3957, Q.3960, T.4991, H.4993 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.3957, L:E.3957, L:T.4991

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

POV.4: 7 residues within 4Å: Chain C: L.4638, L.4642, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.5 Ligand excluded by PLIP POV.5: 14 residues within 4Å: Chain C: W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Chain L: L.4840, N.4847, F.4848 Ligands: POV.4, POV.43 Ligand excluded by PLIP POV.6: 8 residues within 4Å: Chain C: N.4777, S.4778, L.4780, Y.4781, W.4784, M.4808, R.4814 Ligands: POV.7 Ligand excluded by PLIP POV.7: 5 residues within 4Å: Chain C: T.4775, N.4777, L.4780 Ligands: POV.6, POV.8 Ligand excluded by PLIP POV.8: 9 residues within 4Å: Chain C: V.4687, K.4688, W.4691, I.4767, F.4770, G.4771, F.4774, T.4775 Ligands: POV.7 Ligand excluded by PLIP POV.10: 12 residues within 4Å: Chain C: L.4901 Chain F: V.4828, G.4832, A.4835, D.4868, M.4870, T.4871, Y.4873, L.4874, M.4877 Ligands: POV.29, POV.30 Ligand excluded by PLIP POV.11: 10 residues within 4Å: Chain C: F.4912, F.4913 Chain F: T.4821, H.4822, N.4823, G.4824, K.4825, L.4827, V.4828, V.4831 Ligand excluded by PLIP POV.12: 9 residues within 4Å: Chain C: F.4565, F.4569, K.4571, E.4623, E.4624, M.4629 Chain L: D.4868, M.4870 Ligands: POV.41 Ligand excluded by PLIP POV.13: 12 residues within 4Å: Chain C: F.4561, N.4564, F.4565, L.4568, L.4803, I.4806 Chain L: G.4832, A.4835, V.4836, Y.4839, Y.4873 Ligands: POV.41 Ligand excluded by PLIP POV.14: 9 residues within 4Å: Chain C: D.4868, M.4870 Chain F: F.4565, F.4569, K.4571, E.4623, E.4624, M.4629 Ligands: POV.44 Ligand excluded by PLIP POV.15: 12 residues within 4Å: Chain C: G.4832, A.4835, V.4836, Y.4839, Y.4873 Chain F: F.4561, N.4564, F.4565, L.4568, L.4803, I.4806 Ligands: POV.44 Ligand excluded by PLIP POV.19: 7 residues within 4Å: Chain F: L.4638, L.4642, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.20 Ligand excluded by PLIP POV.20: 14 residues within 4Å: Chain C: L.4840, N.4847, F.4848 Chain F: W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Ligands: POV.19, POV.21 Ligand excluded by PLIP POV.21: 10 residues within 4Å: Chain C: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4899, Y.4902, F.4906 Chain F: Y.4620 Ligands: POV.20 Ligand excluded by PLIP POV.22: 8 residues within 4Å: Chain F: N.4777, S.4778, L.4780, Y.4781, W.4784, M.4808, R.4814 Ligands: POV.23 Ligand excluded by PLIP POV.23: 5 residues within 4Å: Chain F: T.4775, N.4777, L.4780 Ligands: POV.22, POV.24 Ligand excluded by PLIP POV.24: 9 residues within 4Å: Chain F: V.4687, K.4688, W.4691, I.4767, F.4770, G.4771, F.4774, T.4775 Ligands: POV.23 Ligand excluded by PLIP POV.26: 10 residues within 4Å: Chain F: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4899, Y.4902, F.4906 Chain I: Y.4620 Ligands: POV.35 Ligand excluded by PLIP POV.27: 12 residues within 4Å: Chain F: L.4901 Chain I: V.4828, G.4832, A.4835, D.4868, M.4870, T.4871, Y.4873, L.4874, M.4877 Ligands: POV.46, POV.47 Ligand excluded by PLIP POV.28: 10 residues within 4Å: Chain F: F.4912, F.4913 Chain I: T.4821, H.4822, N.4823, G.4824, K.4825, L.4827, V.4828, V.4831 Ligand excluded by PLIP POV.29: 9 residues within 4Å: Chain F: D.4868, M.4870 Chain I: F.4565, F.4569, K.4571, E.4623, E.4624, M.4629 Ligands: POV.10 Ligand excluded by PLIP POV.30: 12 residues within 4Å: Chain F: G.4832, A.4835, V.4836, Y.4839, Y.4873 Chain I: F.4561, N.4564, F.4565, L.4568, L.4803, I.4806 Ligands: POV.10 Ligand excluded by PLIP POV.34: 7 residues within 4Å: Chain I: L.4638, L.4642, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.35 Ligand excluded by PLIP POV.35: 14 residues within 4Å: Chain F: L.4840, N.4847, F.4848 Chain I: W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Ligands: POV.26, POV.34 Ligand excluded by PLIP POV.36: 8 residues within 4Å: Chain I: N.4777, S.4778, L.4780, Y.4781, W.4784, M.4808, R.4814 Ligands: POV.37 Ligand excluded by PLIP POV.37: 5 residues within 4Å: Chain I: T.4775, N.4777, L.4780 Ligands: POV.36, POV.38 Ligand excluded by PLIP POV.38: 9 residues within 4Å: Chain I: V.4687, K.4688, W.4691, I.4767, F.4770, G.4771, F.4774, T.4775 Ligands: POV.37 Ligand excluded by PLIP POV.40: 10 residues within 4Å: Chain I: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4899, Y.4902, F.4906 Chain L: Y.4620 Ligands: POV.52 Ligand excluded by PLIP POV.41: 12 residues within 4Å: Chain I: L.4901 Chain L: V.4828, G.4832, A.4835, D.4868, M.4870, T.4871, Y.4873, L.4874, M.4877 Ligands: POV.12, POV.13 Ligand excluded by PLIP POV.42: 10 residues within 4Å: Chain I: F.4912, F.4913 Chain L: T.4821, H.4822, N.4823, G.4824, K.4825, L.4827, V.4828, V.4831 Ligand excluded by PLIP POV.43: 10 residues within 4Å: Chain C: Y.4620 Chain L: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4899, Y.4902, F.4906 Ligands: POV.5 Ligand excluded by PLIP POV.44: 12 residues within 4Å: Chain C: V.4828, G.4832, A.4835, D.4868, M.4870, T.4871, Y.4873, L.4874, M.4877 Chain L: L.4901 Ligands: POV.14, POV.15 Ligand excluded by PLIP POV.45: 10 residues within 4Å: Chain C: T.4821, H.4822, N.4823, G.4824, K.4825, L.4827, V.4828, V.4831 Chain L: F.4912, F.4913 Ligand excluded by PLIP POV.46: 9 residues within 4Å: Chain I: D.4868, M.4870 Chain L: F.4565, F.4569, K.4571, E.4623, E.4624, M.4629 Ligands: POV.27 Ligand excluded by PLIP POV.47: 12 residues within 4Å: Chain I: G.4832, A.4835, V.4836, Y.4839, Y.4873 Chain L: F.4561, N.4564, F.4565, L.4568, L.4803, I.4806 Ligands: POV.27 Ligand excluded by PLIP POV.51: 7 residues within 4Å: Chain L: L.4638, L.4642, V.4787, L.4790, H.4793, Y.4794 Ligands: POV.52 Ligand excluded by PLIP POV.52: 14 residues within 4Å: Chain I: L.4840, N.4847, F.4848 Chain L: W.4784, V.4787, L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Ligands: POV.40, POV.51 Ligand excluded by PLIP POV.53: 8 residues within 4Å: Chain L: N.4777, S.4778, L.4780, Y.4781, W.4784, M.4808, R.4814 Ligands: POV.54 Ligand excluded by PLIP POV.54: 5 residues within 4Å: Chain L: T.4775, N.4777, L.4780 Ligands: POV.53, POV.55 Ligand excluded by PLIP POV.55: 9 residues within 4Å: Chain L: V.4687, K.4688, W.4691, I.4767, F.4770, G.4771, F.4774, T.4775 Ligands: POV.54 Ligand excluded by PLIP

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 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.25: 4 residues within 4Å: Chain F: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4948, F:C.4951, F:H.4968, F:H.4973 ZN.39: 4 residues within 4Å: Chain I: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.4948, I:C.4951, I:H.4968, I:H.4973 ZN.56: 4 residues within 4Å: Chain L: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.4948, L:C.4951, L:H.4968, L:H.4973

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

Nanobody 9657: ADGJ
Peptidyl-prolyl cis-trans isomerase FKBP1B: BEHK
Ryanodine receptor 1: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

D
A

G
D

J
G

B
L

E
B

H
E

K
H

C
J

F
C

I
F

L
I

Membrane

We predict this structure to be a membrane protein.
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Nanobody 9657

Peptidyl-prolyl cis-trans isomerase FKBP1B

Ryanodine receptor 1

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