SMTL ID : 9c1f.1

Mink RyR3 in open conformation bound to Ca2+/ATP/caffeine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.4780, C.4783, H.4800, H.4805 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4780, B:C.4783, B:H.4800, B:H.4805 ZN.7: 4 residues within 4Å: Chain D: C.4780, C.4783, H.4800, H.4805 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.4780, D:C.4783, D:H.4800, D:H.4805 ZN.13: 4 residues within 4Å: Chain F: C.4780, C.4783, H.4800, H.4805 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4780, F:C.4783, F:H.4800, F:H.4805 ZN.19: 4 residues within 4Å: Chain H: C.4780, C.4783, H.4800, H.4805 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4780, H:C.4783, H:H.4800, H:H.4805

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain B: E.3732, E.3806, T.4823 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.3732, B:E.3806, B:E.3806, B:T.4823 CA.8: 3 residues within 4Å: Chain D: E.3732, E.3806, T.4823 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.3732, D:E.3806, D:E.3806, D:T.4823 CA.14: 3 residues within 4Å: Chain F: E.3732, E.3806, T.4823 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.3732, F:E.3806, F:E.3806, F:T.4823 CA.20: 3 residues within 4Å: Chain H: E.3732, E.3806, T.4823 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.3732, H:E.3806, H:E.3806, H:T.4823

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

ATP.3: 16 residues within 4Å: Chain B: K.4050, K.4053, R.4054, I.4057, M.4776, E.4777, K.4779, C.4780, F.4781, I.4782, F.4797, T.4801, L.4802, H.4805, N.4806, L.4807 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:F.4781, B:I.4782, B:T.4801, B:T.4801, B:L.4807 Salt bridges: B:K.4050, B:K.4053, B:K.4053, B:K.4053, B:R.4054 ATP.5: 12 residues within 4Å: Chain B: K.35, T.53, A.56, K.57, P.61, P.268, L.269, R.270, I.271, S.272, R.285, T.313 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.271, B:S.272, B:R.285, B:R.285 Salt bridges: B:K.35, B:K.35 ATP.9: 16 residues within 4Å: Chain D: K.4050, K.4053, R.4054, I.4057, M.4776, E.4777, K.4779, C.4780, F.4781, I.4782, F.4797, T.4801, L.4802, H.4805, N.4806, L.4807 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:F.4781, D:I.4782, D:T.4801, D:T.4801, D:L.4807 Salt bridges: D:K.4050, D:K.4053, D:K.4053, D:K.4053, D:R.4054 ATP.11: 12 residues within 4Å: Chain D: K.35, T.53, A.56, K.57, P.61, P.268, L.269, R.270, I.271, S.272, R.285, T.313 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:I.271, D:S.272, D:R.285, D:R.285 Salt bridges: D:K.35, D:K.35 ATP.15: 16 residues within 4Å: Chain F: K.4050, K.4053, R.4054, I.4057, M.4776, E.4777, K.4779, C.4780, F.4781, I.4782, F.4797, T.4801, L.4802, H.4805, N.4806, L.4807 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:F.4781, F:I.4782, F:T.4801, F:T.4801, F:L.4807 Salt bridges: F:K.4050, F:K.4053, F:K.4053, F:K.4053, F:R.4054 ATP.17: 12 residues within 4Å: Chain F: K.35, T.53, A.56, K.57, P.61, P.268, L.269, R.270, I.271, S.272, R.285, T.313 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:I.271, F:S.272, F:R.285, F:R.285 Salt bridges: F:K.35, F:K.35 ATP.21: 16 residues within 4Å: Chain H: K.4050, K.4053, R.4054, I.4057, M.4776, E.4777, K.4779, C.4780, F.4781, I.4782, F.4797, T.4801, L.4802, H.4805, N.4806, L.4807 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:F.4781, H:I.4782, H:T.4801, H:T.4801, H:L.4807 Salt bridges: H:K.4050, H:K.4053, H:K.4053, H:K.4053, H:R.4054 ATP.23: 12 residues within 4Å: Chain H: K.35, T.53, A.56, K.57, P.61, P.268, L.269, R.270, I.271, S.272, R.285, T.313 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:I.271, H:S.272, H:R.285, H:R.285 Salt bridges: H:K.35, H:K.35

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 10 residues within 4Å: Chain B: F.3598, E.4078, I.4081, F.4082, Q.4085, W.4539, L.4814, I.4818, W.4833, Y.4836 3 PLIP interactions: 3 interactions with chain B pi-Stacking: B:W.4539, B:W.4539, B:W.4539 CFF.10: 10 residues within 4Å: Chain D: F.3598, E.4078, I.4081, F.4082, Q.4085, W.4539, L.4814, I.4818, W.4833, Y.4836 3 PLIP interactions: 3 interactions with chain D pi-Stacking: D:W.4539, D:W.4539, D:W.4539 CFF.16: 10 residues within 4Å: Chain F: F.3598, E.4078, I.4081, F.4082, Q.4085, W.4539, L.4814, I.4818, W.4833, Y.4836 3 PLIP interactions: 3 interactions with chain F pi-Stacking: F:W.4539, F:W.4539, F:W.4539 CFF.22: 10 residues within 4Å: Chain H: F.3598, E.4078, I.4081, F.4082, Q.4085, W.4539, L.4814, I.4818, W.4833, Y.4836 3 PLIP interactions: 3 interactions with chain H pi-Stacking: H:W.4539, H:W.4539, H:W.4539

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain B: R.265, I.289, R.409, R.412 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain D: R.265, I.289, R.409, R.412 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain F: R.265, I.289, R.409, R.412 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain H: R.265, I.289, R.409, R.412 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y.S. et al., Cryo-EM investigation of ryanodine receptor type 3. Nat Commun (2024)

Release Date

2024-10-16

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1B: ACEG
Ryanodine receptor 3: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Membrane

We predict this structure to be a membrane protein.
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Peptidyl-prolyl cis-trans isomerase FKBP1B

Ryanodine receptor 3

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