SMTL ID : 7k0t.1

Cryo-EM structure of rabbit RyR1 in the presence of 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, R.4215, M.4954, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.4211, A:N.4984 Salt bridges: A:K.4214, A:R.4215 ACP.3: 8 residues within 4Å: Chain A: E.4227 Chain B: K.4211, R.4215, M.4954, C.4958, T.4979, N.4984, L.4985 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.4227, A:E.4227, B:K.4211, B:K.4211, B:N.4984 Salt bridges: B:K.4214, B:R.4215 ACP.5: 8 residues within 4Å: Chain C: K.4211, R.4215, M.4954, C.4958, T.4979, N.4984, L.4985 Chain D: E.4227 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.4211, C:N.4984 Salt bridges: C:K.4214, C:R.4215 ACP.7: 10 residues within 4Å: Chain B: E.4227 Chain D: K.4211, K.4214, R.4215, M.4954, K.4957, C.4958, T.4979, N.4984, L.4985 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:K.4211, D:R.4215, D:T.4979, D:N.4984, B:E.4227 Salt bridges: D:K.4214, D:R.4215

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.4958, C.4961, F.4968, 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.4: 4 residues within 4Å: Chain B: C.4958, C.4961, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.4958, B:C.4961, B:H.4983 ZN.6: 6 residues within 4Å: Chain C: C.4958, C.4961, F.4968, H.4978, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4958, C:C.4961, C:H.4978, C:H.4983 ZN.8: 5 residues within 4Å: Chain D: C.4958, C.4961, H.4978, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.4958, D:C.4961, D:H.4978, D:H.4983

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

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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