SMTL ID : 8xkh.1

Structure of chimeric RyR Complex with tetraniliprole

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain I: C.4958, C.4961, F.4968, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.4958, I:C.4961, I:H.4978 ZN.6: 5 residues within 4Å: Chain J: C.4958, C.4961, F.4968, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.4958, J:C.4961, J:H.4978 ZN.11: 5 residues within 4Å: Chain K: C.4958, C.4961, F.4968, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.4958, K:C.4961, K:H.4978 ZN.16: 5 residues within 4Å: Chain L: C.4958, C.4961, F.4968, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.4958, L:C.4961, L:H.4978

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain I: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.3893, I:E.3967, I:T.5001 CA.7: 5 residues within 4Å: Chain J: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.3893, J:E.3967, J:T.5001 CA.12: 5 residues within 4Å: Chain K: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.3893, K:E.3967, K:T.5001 CA.17: 5 residues within 4Å: Chain L: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.3893, L:E.3967, L:T.5001

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

ATP.3: 8 residues within 4Å: Chain I: K.4214, I.4218, M.4954, K.4957, C.4958, T.4979, H.4983, L.4985 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:C.4958 Salt bridges: I:K.4214 ATP.8: 8 residues within 4Å: Chain J: K.4214, I.4218, M.4954, K.4957, C.4958, T.4979, H.4983, L.4985 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:C.4958 Salt bridges: J:K.4214 ATP.13: 6 residues within 4Å: Chain K: K.4214, M.4954, K.4957, C.4958, T.4979, H.4983 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:T.4979 Salt bridges: K:K.4214 ATP.18: 8 residues within 4Å: Chain L: K.4214, I.4218, M.4954, K.4957, C.4958, T.4979, H.4983, L.4985 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:C.4958 Salt bridges: L:K.4214

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 6 residues within 4Å: Chain I: F.3753, I.4242, F.4671, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:Y.5014 pi-Stacking: I:W.4716, I:W.4716, I:W.4716 CFF.9: 6 residues within 4Å: Chain J: F.3753, I.4242, F.4671, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:Y.5014 pi-Stacking: J:W.4716, J:W.4716, J:W.4716 CFF.14: 6 residues within 4Å: Chain K: F.3753, I.4242, F.4671, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:Y.5014 pi-Stacking: K:W.4716, K:W.4716, K:W.4716 CFF.19: 6 residues within 4Å: Chain L: F.3753, I.4242, F.4671, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:Y.5014 pi-Stacking: L:W.4716, L:W.4716, L:W.4716

4 x 01: tetraniliprole

01.5: 14 residues within 4Å: Chain I: Y.4560, K.4563, Y.4564, L.4567, F.4571, I.4657, Y.4791, S.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:Y.4564, I:Y.4791, I:Y.4795 Hydrogen bonds: I:D.4815 pi-Cation interactions: I:K.4563 01.10: 14 residues within 4Å: Chain J: Y.4560, K.4563, Y.4564, L.4567, F.4571, I.4657, Y.4791, S.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.4564, J:Y.4791, J:Y.4795 Hydrogen bonds: J:D.4815 pi-Cation interactions: J:K.4563 01.15: 14 residues within 4Å: Chain K: Y.4560, K.4563, Y.4564, L.4567, F.4571, I.4657, Y.4791, S.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:Y.4564, K:Y.4791, K:Y.4795 Hydrogen bonds: K:D.4815 pi-Cation interactions: K:K.4563 01.20: 14 residues within 4Å: Chain L: Y.4560, K.4563, Y.4564, L.4567, F.4571, I.4657, Y.4791, S.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:Y.4564, L:Y.4791, L:Y.4795 Hydrogen bonds: L:D.4815 pi-Cation interactions: L:K.4563

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

C
I

E
L

G
K

B
F

D
E

F
H

H
G

I
D

J
A

K
B

L
C

Membrane

We predict this structure to be a membrane protein.
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Calmodulin-1

Peptidyl-prolyl cis-trans isomerase FKBP1B

Ryanodine receptor 1

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