SMTL ID : 8dve.1

RyR1 in presence of IpCa-T26E phosphomimetic and activating ligands

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x CFF: CAFFEINE(Non-covalent)

CFF.1: 7 residues within 4Å: Chain A: F.3753, E.4239, I.4242, W.4716, I.4996, W.5011, Y.5014 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:W.4716, A:W.4716 CFF.5: 5 residues within 4Å: Chain D: F.3753, W.4716, I.4996, W.5011, Y.5014 3 PLIP interactions: 3 interactions with chain D pi-Stacking: D:W.4716, D:W.4716, D:W.4716 CFF.9: 6 residues within 4Å: Chain G: F.3753, I.4242, W.4716, I.4996, W.5011, Y.5014 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.5014 pi-Stacking: G:W.4716, G:W.4716, G:W.4716 CFF.13: 5 residues within 4Å: Chain J: F.3753, W.4716, I.4996, W.5011, Y.5014 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:Y.5014 pi-Stacking: J:W.4716, J:W.4716, J:W.4716, J:W.4716

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.3893, E.3967, T.5001 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.3893, A:E.3893, A:E.3967, A:E.3967, A:T.5001 CA.6: 3 residues within 4Å: Chain D: E.3893, E.3967, T.5001 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.3893, D:E.3893, D:E.3967, D:E.3967, D:T.5001 CA.10: 3 residues within 4Å: Chain G: E.3893, E.3967, T.5001 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.3893, G:E.3893, G:E.3967, G:E.3967, G:T.5001 CA.14: 5 residues within 4Å: Chain J: E.3893, H.3895, E.3967, Q.3970, T.5001 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.3893, J:E.3893, J:E.3967, J:E.3967, J:T.5001

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

ATP.3: 11 residues within 4Å: Chain A: K.4214, R.4215, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, N.4984, L.4985 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.4959, A:I.4960, A:T.4979, A:L.4985 Salt bridges: A:K.4214, A:R.4215, A:R.4215 ATP.7: 9 residues within 4Å: Chain D: K.4214, R.4215, M.4954, E.4955, C.4958, F.4959, F.4975, T.4979, H.4983 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:F.4959, D:T.4979 Salt bridges: D:K.4214, D:K.4214, D:R.4215, D:R.4215 ATP.11: 10 residues within 4Å: Chain G: K.4214, R.4215, M.4954, E.4955, C.4958, F.4959, F.4975, T.4979, H.4983, L.4985 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:F.4959, G:T.4979 Salt bridges: G:K.4214, G:K.4214, G:R.4215 ATP.15: 10 residues within 4Å: Chain J: K.4211, K.4214, R.4215, M.4954, C.4958, I.4960, F.4975, T.4979, H.4983, L.4985 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:H.4983, J:L.4985 Salt bridges: J:K.4211, J:K.4214, J:R.4215, J:R.4215

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.4961, F.4968, H.4978, H.4983, C.5027 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.4961, A:H.4978, A:H.4983 ZN.8: 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 ZN.12: 4 residues within 4Å: Chain G: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4958, G:C.4961, G:H.4978, G:H.4983 ZN.16: 5 residues within 4Å: Chain J: C.4958, C.4961, H.4978, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4961, J:H.4978, J:H.4983, J:C.5027

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: ADGJ
Peptidyl-prolyl cis-trans isomerase FKBP1B: BEHK
Calmodulin-1: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
A

G
G

J
J

B
E

E
B

H
H

K
K

C
F

F
C

I
I

L
L

Membrane

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

Peptidyl-prolyl cis-trans isomerase FKBP1B

Calmodulin-1

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