SMTL ID : 8drp.1

Focus/local refined map in C4 of signal subtracted RyR1 particles

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x CFF: CAFFEINE(Non-covalent)

CFF.1: 6 residues within 4Å: Chain A: E.4239, I.4242, W.4716, I.4996, W.5011, Y.5014 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.4239, A:Y.5014 pi-Stacking: A:W.4716, A:W.4716 CFF.4: 6 residues within 4Å: Chain B: E.4239, I.4242, W.4716, I.4996, W.5011, Y.5014 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.4239, B:Y.5014 pi-Stacking: B:W.4716, B:W.4716 CFF.7: 6 residues within 4Å: Chain C: E.4239, I.4242, W.4716, I.4996, W.5011, Y.5014 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.4239, C:Y.5014 pi-Stacking: C:W.4716, C:W.4716 CFF.10: 6 residues within 4Å: Chain D: E.4239, I.4242, W.4716, I.4996, W.5011, Y.5014 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.4239, D:Y.5014 pi-Stacking: D:W.4716, D:W.4716

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

ATP.2: 10 residues within 4Å: Chain A: R.4215, M.4954, E.4955, C.4958, F.4959, I.4960, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.4959, A:H.4983, A:L.4985 Salt bridges: A:K.4211, A:R.4215 ATP.5: 10 residues within 4Å: Chain B: R.4215, M.4954, E.4955, C.4958, F.4959, I.4960, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.4959, B:H.4983, B:L.4985 Salt bridges: B:K.4211, B:R.4215 ATP.8: 10 residues within 4Å: Chain C: R.4215, M.4954, E.4955, C.4958, F.4959, I.4960, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.4959, C:H.4983, C:L.4985 Salt bridges: C:K.4211, C:R.4215 ATP.11: 10 residues within 4Å: Chain D: R.4215, M.4954, E.4955, C.4958, F.4959, I.4960, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:F.4959, D:H.4983, D:L.4985 Salt bridges: D:K.4211, D:R.4215

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.4958, I.4960, 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.6: 5 residues within 4Å: Chain B: C.4958, I.4960, 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 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4958, C:C.4961, C:H.4978, C:H.4983 ZN.12: 5 residues within 4Å: Chain D: C.4958, I.4960, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haji-Ghassemi, O. et al., Cryo-EM analysis of scorpion toxin binding to Ryanodine Receptors reveals subconductance that is abolished by PKA phosphorylation. Sci Adv (2023)

Release Date

2023-05-31

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

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