SMTL ID : 7tdg.1

Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in inactivated conformation (Dataset-A)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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 B: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4958, B:C.4961, B:H.4978, B:H.4983 ZN.14: 4 residues within 4Å: Chain C: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4958, C:C.4961, C:H.4978, C:H.4983 ZN.19: 4 residues within 4Å: Chain D: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.4958, D:C.4961, D:H.4978, D:H.4983

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3893, A:E.3967, A:T.5001 CA.3: 1 residues within 4Å: Chain A: L.4980 No protein-ligand interaction detected (PLIP) CA.8: 4 residues within 4Å: Chain B: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.3893, B:E.3967, B:T.5001 CA.9: 1 residues within 4Å: Chain B: L.4980 No protein-ligand interaction detected (PLIP) CA.15: 4 residues within 4Å: Chain C: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.3893, C:E.3967, C:T.5001 CA.16: 1 residues within 4Å: Chain C: L.4980 No protein-ligand interaction detected (PLIP) CA.20: 4 residues within 4Å: Chain D: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.3893, D:E.3967, D:T.5001 CA.21: 1 residues within 4Å: Chain D: L.4980 No protein-ligand interaction detected (PLIP)

4 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.4: 9 residues within 4Å: Chain A: M.4954, E.4955, K.4957, C.4958, F.4975, T.4979, H.4983, N.4984, L.4985 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.4983 ACP.10: 8 residues within 4Å: Chain B: M.4954, E.4955, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.4984 ACP.17: 7 residues within 4Å: Chain C: R.4215, M.4954, C.4958, T.4979, H.4983, N.4984, L.4985 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.4215, C:T.4979, C:N.4984 ACP.22: 7 residues within 4Å: Chain D: M.4954, E.4955, C.4958, T.4979, H.4983, N.4984, L.4985 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.4984

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

POV.5: 8 residues within 4Å: Chain A: N.4806, F.4807, F.4808, A.4811, L.4814 Chain C: V.4853, N.4857 Ligands: POV.18 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.4807, A:F.4808, A:A.4811, A:L.4814, C:V.4853 POV.6: 7 residues within 4Å: Chain A: Y.4851, N.4857, F.4858, Y.4909, Y.4912 Chain D: Y.4629 Ligands: POV.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.4851, A:F.4858, A:F.4858, A:F.4858, A:Y.4912 POV.11: 8 residues within 4Å: Chain B: N.4806, F.4807, F.4808, A.4811, L.4814 Chain D: V.4853, N.4857 Ligands: POV.24 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:V.4853, B:F.4807, B:F.4808, B:A.4811, B:L.4814 POV.12: 7 residues within 4Å: Chain B: Y.4851, N.4857, F.4858, Y.4909, Y.4912 Chain C: Y.4629 Ligands: POV.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.4851, B:F.4858, B:F.4858, B:Y.4912 POV.13: 9 residues within 4Å: Chain B: V.4853, V.4854, N.4857, F.4858 Chain C: N.4806, F.4807, F.4808, A.4811 Ligands: POV.12 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.4807, C:F.4808, C:A.4811, B:V.4853, B:V.4854, B:F.4858, B:F.4858 POV.18: 6 residues within 4Å: Chain A: Y.4629 Chain C: Y.4851, F.4858, Y.4909, Y.4912 Ligands: POV.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.4851, C:F.4858, C:F.4858, C:F.4858, C:Y.4912 POV.23: 8 residues within 4Å: Chain A: V.4853, N.4857 Chain D: N.4806, F.4807, F.4808, A.4811, L.4814 Ligands: POV.6 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:V.4853, D:F.4807, D:F.4808, D:A.4811, D:L.4814 POV.24: 7 residues within 4Å: Chain B: Y.4629 Chain D: Y.4851, N.4857, F.4858, Y.4909, Y.4912 Ligands: POV.11 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.4851, D:F.4858, D:F.4858, D:F.4858, D:Y.4912

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayak, A.R. et al., Ca 2+ -inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM. Elife (2022)

Release Date

2022-03-09

Peptides

Ryanodine receptor 1,RyR1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Membrane

We predict this structure to be a membrane protein.
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Ryanodine receptor 1,RyR1

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