SMTL ID : 8xlh.1

Structure of chimeric RyR-I4657M/G4819E

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.4958, 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.4978 ZN.5: 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.4978 ZN.9: 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.4978 ZN.13: 4 residues within 4Å: Chain J: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4958, J:C.4961, J:H.4978, J:H.4978

4 x CA: CALCIUM ION(Non-covalent)

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

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

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

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 6 residues within 4Å: Chain A: F.3753, E.4239, I.4242, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain A pi-Stacking: A:W.4716, A:W.4716, A:W.4716 CFF.8: 6 residues within 4Å: Chain D: F.3753, E.4239, I.4242, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain D pi-Stacking: D:W.4716, D:W.4716, D:W.4716 CFF.12: 6 residues within 4Å: Chain G: F.3753, E.4239, I.4242, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain G pi-Stacking: G:W.4716, G:W.4716, G:W.4716 CFF.16: 6 residues within 4Å: Chain J: F.3753, E.4239, I.4242, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain J pi-Stacking: J:W.4716, J:W.4716, J: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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
C

J
B

B
E

E
H

H
G

K
F

C
I

F
L

I
K

L
J

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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