SMTL ID : 9e1e.1

Structure of RyR1 in the primed state in the presence of uracil

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.4215, A:R.4215, A:F.4959, A:I.4960, A:H.4983, A:L.4985 Salt bridges: A:K.4211, A:K.4211, A:K.4214, A:K.4214 ATP.5: 14 residues within 4Å: Chain F: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:R.4215, F:R.4215, F:F.4959, F:I.4960, F:H.4983, F:L.4985 Salt bridges: F:K.4211, F:K.4211, F:K.4214, F:K.4214, F:K.4214 ATP.9: 14 residues within 4Å: Chain G: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:R.4215, G:R.4215, G:F.4959, G:I.4960, G:H.4983, G:L.4985 Salt bridges: G:K.4211, G:K.4211, G:K.4214, G:K.4214 ATP.13: 14 residues within 4Å: Chain H: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:R.4215, H:R.4215, H:F.4959, H:I.4960, H:H.4983, H:L.4985 Salt bridges: H:K.4211, H:K.4211, H:K.4214, H:K.4214

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.3893, A:E.3967, A:E.3967, A:T.5001 CA.6: 3 residues within 4Å: Chain F: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.3893, F:E.3967, F:E.3967, F:T.5001 CA.10: 3 residues within 4Å: Chain G: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3893, G:E.3967, G:E.3967, G:T.5001 CA.14: 3 residues within 4Å: Chain H: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.3893, H:E.3967, H:E.3967, H:T.5001

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4958, A:C.4961, A:H.4978, A:H.4983 ZN.7: 4 residues within 4Å: Chain F: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4958, F:C.4961, F:H.4978, F:H.4983 ZN.11: 4 residues within 4Å: Chain G: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4958, G:C.4961, G:H.4978, G:H.4983 ZN.15: 4 residues within 4Å: Chain H: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4958, H:C.4961, H:H.4978, H:H.4983

4 x URA: URACIL(Non-covalent)

URA.4: 5 residues within 4Å: Chain A: F.3753, I.4242, W.4716, I.4996, Y.5014 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.3753, A:W.4716, A:I.4996 Hydrogen bonds: A:Y.5014 pi-Stacking: A:W.4716 URA.8: 5 residues within 4Å: Chain F: F.3753, I.4242, W.4716, I.4996, Y.5014 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:W.4716, F:I.4996 Hydrogen bonds: F:Y.5014, F:Y.5014 pi-Stacking: F:W.4716 URA.12: 5 residues within 4Å: Chain G: F.3753, I.4242, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:W.4716, G:I.4996 Hydrogen bonds: G:Y.5014 pi-Stacking: G:W.4716 URA.16: 5 residues within 4Å: Chain H: F.3753, I.4242, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:W.4716, H:I.4996 Hydrogen bonds: H:Y.5014 pi-Stacking: H:W.4716

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miotto, M.C. et al., Targeting ryanodine receptors with allopurinol and xanthine derivatives for the treatment of cardiac and musculoskeletal weakness disorders. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2024-10-30

Peptides

Ryanodine receptor 1: AFGH
Peptidyl-prolyl cis-trans isomerase FKBP1A: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

G
D

H
C

B
E

C
H

D
G

E
F

Membrane

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

Peptidyl-prolyl cis-trans isomerase FKBP1A

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