SMTL ID : 8y40.1

Structure of chimeric RyR-I4657M/G4819E complex with chlorantraniliprole

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x F0U: 5-bromanyl-N-[4-chloranyl-2-methyl-6-(methylcarbamoyl)phenyl]-2-(3-chloranylpyridin-2-yl)pyrazole-3-carboxamide(Non-covalent)

F0U.1: 12 residues within 4Å: Chain I: Y.4560, K.4563, Y.4564, L.4567, M.4657, Y.4791, S.4792, Y.4795, D.4815, M.4818, E.4819, V.4820 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:Y.4560, I:Y.4564, I:Y.4791 Hydrogen bonds: I:K.4563, I:D.4815, I:D.4815 pi-Stacking: I:Y.4795 pi-Cation interactions: I:K.4563 F0U.6: 12 residues within 4Å: Chain J: Y.4560, K.4563, Y.4564, L.4567, M.4657, Y.4791, S.4792, Y.4795, D.4815, M.4818, E.4819, V.4820 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:Y.4560, J:Y.4564, J:Y.4791 Hydrogen bonds: J:K.4563, J:D.4815, J:D.4815 pi-Stacking: J:Y.4795 pi-Cation interactions: J:K.4563 F0U.11: 12 residues within 4Å: Chain K: Y.4560, K.4563, Y.4564, L.4567, M.4657, Y.4791, S.4792, Y.4795, D.4815, M.4818, E.4819, V.4820 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:Y.4560, K:Y.4564, K:Y.4791 Hydrogen bonds: K:K.4563, K:D.4815, K:D.4815 pi-Stacking: K:Y.4795 pi-Cation interactions: K:K.4563 F0U.16: 12 residues within 4Å: Chain L: Y.4560, K.4563, Y.4564, L.4567, M.4657, Y.4791, S.4792, Y.4795, D.4815, M.4818, E.4819, V.4820 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:Y.4560, L:Y.4564, L:Y.4791 Hydrogen bonds: L:K.4563, L:D.4815, L:D.4815 pi-Stacking: L:Y.4795 pi-Cation interactions: L:K.4563

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain I: C.4958, C.4961, F.4968, H.4978, H.4983 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.4961, I:H.4978 ZN.7: 5 residues within 4Å: Chain J: C.4958, C.4961, F.4968, H.4978, H.4983 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.4961, J:H.4978 ZN.12: 5 residues within 4Å: Chain K: C.4958, C.4961, F.4968, H.4978, H.4983 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.4961, K:H.4978 ZN.17: 5 residues within 4Å: Chain L: C.4958, C.4961, F.4968, H.4978, H.4983 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:C.4961, L:H.4978

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain I: E.3893, E.3967, T.5001 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:E.3967, I:T.5001 CA.8: 3 residues within 4Å: Chain J: E.3893, E.3967, T.5001 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.3967, J:T.5001 CA.13: 3 residues within 4Å: Chain K: E.3893, E.3967, T.5001 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.3967, K:T.5001 CA.18: 3 residues within 4Å: Chain L: E.3893, E.3967, T.5001 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:E.3967, L:T.5001

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

ATP.4: 12 residues within 4Å: Chain I: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:M.4954, I:F.4959, I:H.4983 Salt bridges: I:K.4211, I:K.4211, I:K.4214, I:K.4214 ATP.9: 13 residues within 4Å: Chain J: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, L.4980, H.4983, N.4984, L.4985 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:M.4954, J:F.4959, J:H.4983 Salt bridges: J:K.4211, J:K.4211, J:K.4214, J:K.4214 ATP.14: 14 residues within 4Å: Chain K: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, E.4976, T.4979, L.4980, H.4983, N.4984, L.4985 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:M.4954, K:F.4959, K:H.4983 Salt bridges: K:K.4211, K:K.4211, K:K.4214, K:K.4214 ATP.19: 13 residues within 4Å: Chain L: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, L.4980, H.4983, N.4984, L.4985 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:M.4954, L:F.4959, L:H.4983 Salt bridges: L:K.4211, L:K.4211, L:K.4214, L:K.4214

4 x CFF: CAFFEINE(Non-covalent)

CFF.5: 8 residues within 4Å: Chain I: F.3753, E.4239, I.4242, W.4716, L.4992, I.4996, W.5011, Y.5014 4 PLIP interactions: 4 interactions with chain I pi-Stacking: I:W.4716, I:W.4716, I:W.4716, I:W.4716 CFF.10: 8 residues within 4Å: Chain J: F.3753, E.4239, I.4242, Q.4246, W.4716, L.4992, I.4996, W.5011 4 PLIP interactions: 4 interactions with chain J pi-Stacking: J:W.4716, J:W.4716, J:W.4716, J:W.4716 CFF.15: 7 residues within 4Å: Chain K: F.3753, E.4239, I.4242, W.4716, L.4992, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain K pi-Stacking: K:W.4716, K:W.4716, K:W.4716 CFF.20: 6 residues within 4Å: Chain L: F.3753, I.4242, W.4716, L.4992, I.4996, W.5011 4 PLIP interactions: 4 interactions with chain L pi-Stacking: L:W.4716, L:W.4716, L:W.4716, L:W.4716

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, L. et al., Cryo-EM structures of ryanodine receptors and diamide insecticides reveal the mechanisms of selectivity and resistance. Nat Commun (2024)

Release Date

2024-10-30

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1B: ACEG
Calmodulin-1: BDFH
Ryanodine receptor 1: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
H

E
G

G
F

B
I

D
L

F
K

H
J

I
A

J
B

K
C

L
D

Membrane

We predict this structure to be a membrane protein.
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Peptidyl-prolyl cis-trans isomerase FKBP1B

Calmodulin-1

Ryanodine receptor 1

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