SMTL ID : 7umz.1

Cryo-EM structure of rabbit RyR1 in the presence of high Mg2+ and AMP-PCP in nanodisc

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

ACP.1: 11 residues within 4Å: Chain A: K.4211, R.4215, M.4954, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 Ligands: MG.5, MG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.4211, A:R.4215, A:C.4958, A:N.4984 Salt bridges: A:K.4214 ACP.9: 11 residues within 4Å: Chain B: K.4211, R.4215, M.4954, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 Ligands: MG.12, MG.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.4211, B:R.4215, B:C.4958, B:N.4984 Salt bridges: B:K.4214 ACP.16: 10 residues within 4Å: Chain C: K.4211, R.4215, M.4954, C.4958, T.4979, H.4983, N.4984, L.4985 Ligands: MG.19, MG.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.4211, C:R.4215 Salt bridges: C:K.4214 ACP.23: 9 residues within 4Å: Chain D: K.4211, R.4215, C.4958, T.4979, H.4983, N.4984, L.4985 Ligands: MG.26, MG.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.4211, D:R.4215, D:N.4984

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.10: 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.17: 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.24: 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

13 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain A: E.3967, Q.3970 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.3967, H2O.1 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: ACP.1 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ACP.1 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: E.3967, Q.3970 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.3967, H2O.1 MG.12: 1 residues within 4Å: Ligands: ACP.9 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ACP.9 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain C: E.3967, Q.3970 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.3967, H2O.1 MG.19: 1 residues within 4Å: Ligands: ACP.16 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: ACP.16 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain D: E.3967, Q.3970 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.3967, H2O.1 MG.26: 1 residues within 4Å: Ligands: ACP.23 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Ligands: ACP.23 No protein-ligand interaction detected (PLIP)

8 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.7: 13 residues within 4Å: Chain A: W.4794, Y.4804, N.4805, N.4806, F.4807, F.4808, A.4810, A.4811, L.4814 Chain D: L.4850, N.4857, F.4858 Ligands: LBN.29 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.4794, A:Y.4804, A:F.4807, A:A.4810, A:A.4811, A:L.4814, D:L.4850, D:F.4858, D:F.4858 Hydrogen bonds: A:Y.4804, A:N.4806, A:F.4807 LBN.8: 6 residues within 4Å: Chain A: Y.4851, V.4854, F.4858, F.4859, Y.4909 Ligands: LBN.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.4851, A:Y.4851, A:V.4854, A:V.4854, A:F.4858, A:F.4858, A:F.4858, A:F.4859 LBN.14: 8 residues within 4Å: Chain B: Y.4851, V.4854, N.4857, F.4858, Y.4909, F.4916 Chain C: Y.4629 Ligands: LBN.21 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.4851, B:V.4854, B:F.4858, B:F.4858, B:F.4916 Hydrogen bonds: B:Y.4909 LBN.15: 14 residues within 4Å: Chain A: V.4854, N.4857, F.4858 Chain B: M.4798, L.4801, Y.4804, N.4805, N.4806, F.4807, F.4808, A.4810, A.4811, L.4814 Ligands: LBN.8 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.4854, A:F.4858, B:L.4801, B:Y.4804, B:F.4807, B:F.4808, B:A.4810, B:A.4811, B:L.4814 Hydrogen bonds: A:N.4857, B:N.4806, B:N.4806, B:F.4807 LBN.21: 13 residues within 4Å: Chain B: L.4850, N.4857, F.4858 Chain C: W.4794, Y.4804, N.4805, N.4806, F.4807, F.4808, A.4810, A.4811, L.4814 Ligands: LBN.14 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.4794, C:Y.4804, C:F.4807, C:F.4808, C:A.4810, C:A.4811, C:L.4814, B:L.4850, B:F.4858, B:F.4858 Hydrogen bonds: C:Y.4804, C:N.4806, C:F.4807 LBN.22: 7 residues within 4Å: Chain C: Y.4851, V.4854, N.4857, F.4858, F.4859, Y.4909 Ligands: LBN.28 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.4851, C:Y.4851, C:V.4854, C:V.4854, C:F.4858, C:F.4858, C:F.4858, C:F.4859 LBN.28: 12 residues within 4Å: Chain C: N.4857, F.4858 Chain D: M.4798, L.4801, Y.4804, N.4805, N.4806, F.4807, F.4808, A.4811, L.4814 Ligands: LBN.22 12 PLIP interactions: 2 interactions with chain C, 10 interactions with chain D Hydrophobic interactions: C:F.4858, D:L.4801, D:Y.4804, D:F.4807, D:F.4808, D:F.4808, D:A.4811, D:L.4814 Hydrogen bonds: C:N.4857, D:Y.4804, D:Y.4804, D:N.4806 LBN.29: 8 residues within 4Å: Chain A: Y.4629 Chain D: Y.4851, V.4854, N.4857, F.4858, Y.4909, F.4916 Ligands: LBN.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.4851, D:V.4854, D:F.4858, D:F.4916 Hydrogen bonds: D:Y.4909

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayak, A.R. et al., Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor. Biorxiv (2024)

Release Date

2023-04-12

Peptides

Ryanodine receptor 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

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