SMTL ID : 9rcw.1

Primed-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

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.12: 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.21: 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.31: 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

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

ATP.2: 12 residues within 4Å: Chain C: K.4201, K.4204, R.4205, M.4944, 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:K.4201, C:F.4949, C:L.4975 Salt bridges: C:K.4201, C:K.4201, C:K.4204, C:K.4204, C:R.4205 ATP.13: 12 residues within 4Å: Chain F: K.4201, K.4204, R.4205, M.4944, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:K.4201, F:F.4949, F:L.4975 Salt bridges: F:K.4201, F:K.4201, F:K.4204, F:K.4204, F:R.4205 ATP.22: 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:K.4201, I:F.4949, I:I.4950, I:L.4975 Salt bridges: I:K.4201, I:K.4201, I:K.4204, I:K.4204, I:R.4205 ATP.32: 12 residues within 4Å: Chain L: K.4201, K.4204, R.4205, M.4944, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:K.4201, L:F.4949, L:L.4975 Salt bridges: L:K.4201, L:K.4201, L:K.4204, L:K.4204, L:R.4205

4 x CFF: CAFFEINE(Non-covalent)

CFF.3: 6 residues within 4Å: Chain C: F.3743, E.4229, I.4232, W.4706, I.4986, W.5001 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.4229 pi-Stacking: C:W.4706, C:W.4706, C:W.4706 CFF.14: 6 residues within 4Å: Chain F: F.3743, E.4229, I.4232, W.4706, I.4986, W.5001 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.4229 pi-Stacking: F:W.4706, F:W.4706, F:W.4706 CFF.23: 6 residues within 4Å: Chain I: F.3743, E.4229, I.4232, W.4706, I.4986, W.5001 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:E.4229 pi-Stacking: I:W.4706, I:W.4706, I:W.4706 CFF.33: 6 residues within 4Å: Chain L: F.3743, E.4229, I.4232, W.4706, I.4986, W.5001 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:E.4229 pi-Stacking: L:W.4706, L:W.4706, L:W.4706

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain C: E.3883, E.3957, Q.3960, 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.15: 4 residues within 4Å: Chain F: E.3883, E.3957, Q.3960, T.4991 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.3883, F:E.3957, F:E.3957, F:T.4991 CA.24: 4 residues within 4Å: Chain I: E.3883, E.3957, Q.3960, T.4991 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.3883, I:E.3957, I:E.3957, I:T.4991 CA.34: 4 residues within 4Å: Chain L: E.3883, E.3957, Q.3960, T.4991 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.3883, L:E.3957, L:E.3957, L:T.4991

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

POV.5: 5 residues within 4Å: Chain C: L.4638, L.4790, L.4791, H.4793 Ligands: POV.6 Ligand excluded by PLIP POV.6: 12 residues within 4Å: Chain C: L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Chain L: V.4843, N.4847, F.4848 Ligands: POV.5, POV.7 Ligand excluded by PLIP POV.7: 8 residues within 4Å: Chain C: Y.4620 Chain L: Y.4841, V.4844, N.4847, F.4848, Y.4899, Y.4902 Ligands: POV.6 Ligand excluded by PLIP POV.8: 7 residues within 4Å: Chain C: M.4829, G.4832, A.4835, Y.4873 Chain F: F.4561, N.4564, F.4565 Ligand excluded by PLIP POV.9: 5 residues within 4Å: Chain C: T.4821, H.4822, G.4824, K.4825, V.4831 Ligand excluded by PLIP POV.10: 8 residues within 4Å: Chain C: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, G.4771, T.4775 Ligand excluded by PLIP POV.11: 9 residues within 4Å: Chain F: Y.4841, V.4844, N.4847, F.4848, F.4849, Y.4899, Y.4902 Chain I: Y.4620 Ligands: POV.26 Ligand excluded by PLIP POV.16: 5 residues within 4Å: Chain F: L.4638, L.4790, L.4791, H.4793 Ligands: POV.17 Ligand excluded by PLIP POV.17: 12 residues within 4Å: Chain C: V.4843, N.4847, F.4848 Chain F: L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Ligands: POV.16, POV.18 Ligand excluded by PLIP POV.18: 8 residues within 4Å: Chain C: Y.4841, V.4844, N.4847, F.4848, Y.4899, Y.4902 Chain F: Y.4620 Ligands: POV.17 Ligand excluded by PLIP POV.19: 5 residues within 4Å: Chain F: T.4821, H.4822, G.4824, K.4825, V.4831 Ligand excluded by PLIP POV.20: 8 residues within 4Å: Chain F: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, G.4771, T.4775 Ligand excluded by PLIP POV.25: 7 residues within 4Å: Chain I: L.4638, T.4641, L.4790, L.4791, H.4793, Y.4794 Ligands: POV.26 Ligand excluded by PLIP POV.26: 12 residues within 4Å: Chain F: V.4843, N.4847, F.4848 Chain I: L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Ligands: POV.11, POV.25 Ligand excluded by PLIP POV.27: 8 residues within 4Å: Chain I: M.4829, G.4832, A.4835, Y.4873 Chain L: F.4561, N.4564, F.4565, L.4803 Ligand excluded by PLIP POV.28: 6 residues within 4Å: Chain I: T.4821, H.4822, G.4824, K.4825, L.4827, V.4831 Ligand excluded by PLIP POV.29: 8 residues within 4Å: Chain I: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, G.4771, T.4775 Ligand excluded by PLIP POV.30: 7 residues within 4Å: Chain F: M.4829, G.4832, A.4835, Y.4873 Chain I: F.4561, N.4564, F.4565 Ligand excluded by PLIP POV.35: 5 residues within 4Å: Chain L: L.4638, L.4790, L.4791, H.4793 Ligands: POV.36 Ligand excluded by PLIP POV.36: 12 residues within 4Å: Chain I: V.4843, N.4847, F.4848 Chain L: L.4791, Y.4794, N.4795, F.4797, F.4798, A.4801, L.4804 Ligands: POV.35, POV.37 Ligand excluded by PLIP POV.37: 8 residues within 4Å: Chain I: Y.4841, V.4844, N.4847, F.4848, Y.4899, Y.4902 Chain L: Y.4620 Ligands: POV.36 Ligand excluded by PLIP POV.38: 7 residues within 4Å: Chain C: F.4561, N.4564, F.4565 Chain L: M.4829, G.4832, A.4835, Y.4873 Ligand excluded by PLIP POV.39: 5 residues within 4Å: Chain L: T.4821, H.4822, G.4824, K.4825, V.4831 Ligand excluded by PLIP POV.40: 8 residues within 4Å: Chain L: R.4663, D.4685, D.4686, V.4687, K.4688, W.4691, G.4771, T.4775 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

D
K

G
D

J
B

B
I

E
L

H
E

K
F

C
G

F
J

I
C

L
A

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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