SMTL ID : 7k0s.1

Cryo-EM structure of rabbit RyR1 in the presence of 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: 10 residues within 4Å: Chain A: K.4211, K.4214, M.4954, C.4958, T.4979, H.4983, N.4984, L.4985 Chain C: E.4227 Ligands: MG.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.4211, A:T.4979, A:H.4983 Salt bridges: A:K.4211, A:K.4214 ACP.4: 10 residues within 4Å: Chain B: K.4211, K.4214, R.4215, M.4954, C.4958, T.4979, H.4983, N.4984, L.4985 Ligands: MG.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.4211, B:R.4215, B:R.4215, B:H.4983 Salt bridges: B:K.4214 ACP.8: 10 residues within 4Å: Chain C: K.4211, K.4214, R.4215, M.4954, C.4958, F.4975, E.4976, T.4979, L.4985 Ligands: MG.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.4215, C:C.4958, C:E.4976 Salt bridges: C:K.4211, C:K.4214 ACP.11: 12 residues within 4Å: Chain B: E.4227 Chain D: K.4211, K.4214, M.4954, K.4957, C.4958, F.4975, T.4979, H.4983, N.4984, L.4985 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.4211, D:N.4984 Salt bridges: D:K.4211, D:K.4214

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.5: 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.9: 5 residues within 4Å: Chain C: C.4958, I.4960, C.4961, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.4958, C:C.4961, C:H.4983 ZN.12: 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

5 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ACP.4 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ACP.11 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ACP.1 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ACP.8 No protein-ligand interaction detected (PLIP)

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

2021-09-22

Peptides

RyR1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

Membrane

We predict this structure to be a membrane protein.
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RyR1

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