SMTL ID : 7ua4.1

Structure of PKA phosphorylated human RyR2-R2474S in the open state in the presence of Calmodulin

Coordinates

PDB Format

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.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4888, A:C.4891, A:H.4908, A:H.4913 ZN.6: 4 residues within 4Å: Chain J: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4888, J:C.4891, J:H.4908, J:H.4913 ZN.11: 4 residues within 4Å: Chain K: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.4888, K:C.4891, K:H.4908, K:H.4913 ZN.16: 4 residues within 4Å: Chain L: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.4888, L:C.4891, L:H.4908, L:H.4913

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

ATP.2: 13 residues within 4Å: Chain A: K.4166, K.4169, R.4170, M.4884, E.4885, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:F.4889, A:I.4890, A:H.4913, A:L.4915 Salt bridges: A:K.4166, A:K.4166, A:K.4169, A:K.4169, A:R.4170, A:R.4170 ATP.5: 9 residues within 4Å: Chain A: W.893, K.897, W.902, H.915, Y.931, M.935, W.1007, R.1011, R.1031 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.893, A:Y.931, A:W.1007, A:R.1031, A:N.1046 Salt bridges: A:R.1011 pi-Stacking: A:W.902, A:W.902 ATP.7: 13 residues within 4Å: Chain J: K.4166, K.4169, R.4170, M.4884, E.4885, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:F.4889, J:I.4890, J:H.4913, J:L.4915 Salt bridges: J:K.4166, J:K.4166, J:K.4169, J:K.4169, J:R.4170, J:R.4170 ATP.10: 9 residues within 4Å: Chain J: W.893, K.897, W.902, H.915, Y.931, M.935, W.1007, R.1011, R.1031 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:W.893, J:Y.931, J:W.1007, J:R.1031, J:N.1046 Salt bridges: J:R.1011 pi-Stacking: J:W.902, J:W.902 ATP.12: 13 residues within 4Å: Chain K: K.4166, K.4169, R.4170, M.4884, E.4885, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:F.4889, K:I.4890, K:H.4913, K:L.4915 Salt bridges: K:K.4166, K:K.4166, K:K.4169, K:K.4169, K:R.4170, K:R.4170 ATP.15: 9 residues within 4Å: Chain K: W.893, K.897, W.902, H.915, Y.931, M.935, W.1007, R.1011, R.1031 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:W.893, K:Y.931, K:W.1007, K:R.1031, K:N.1046 Salt bridges: K:R.1011 pi-Stacking: K:W.902, K:W.902 ATP.17: 13 residues within 4Å: Chain L: K.4166, K.4169, R.4170, M.4884, E.4885, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:F.4889, L:I.4890, L:H.4913, L:L.4915 Salt bridges: L:K.4166, L:K.4166, L:K.4169, L:K.4169, L:R.4170, L:R.4170 ATP.20: 9 residues within 4Å: Chain L: W.893, K.897, W.902, H.915, Y.931, M.935, W.1007, R.1011, R.1031 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:W.893, L:Y.931, L:W.1007, L:R.1031, L:N.1046 Salt bridges: L:R.1011 pi-Stacking: L:W.902, L:W.902

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: E.3848, E.3922, T.4931 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3848, A:E.3922, A:T.4931 CA.8: 3 residues within 4Å: Chain J: E.3848, E.3922, T.4931 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.3848, J:E.3922, J:T.4931 CA.13: 3 residues within 4Å: Chain K: E.3848, E.3922, T.4931 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.3848, K:E.3922, K:T.4931 CA.18: 3 residues within 4Å: Chain L: E.3848, E.3922, T.4931 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.3848, L:E.3922, L:T.4931

4 x XAN: XANTHINE(Non-covalent)

XAN.4: 6 residues within 4Å: Chain A: E.4194, I.4197, W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.4944, A:Y.4944 pi-Stacking: A:W.4645, A:W.4645, A:W.4645 XAN.9: 6 residues within 4Å: Chain J: E.4194, I.4197, W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:Y.4944, J:Y.4944 pi-Stacking: J:W.4645, J:W.4645, J:W.4645 XAN.14: 6 residues within 4Å: Chain K: E.4194, I.4197, W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:Y.4944, K:Y.4944 pi-Stacking: K:W.4645, K:W.4645, K:W.4645 XAN.19: 6 residues within 4Å: Chain L: E.4194, I.4197, W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:Y.4944, L:Y.4944 pi-Stacking: L:W.4645, L:W.4645, L:W.4645

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miotto, M.C. et al., Structural analyses of human ryanodine receptor type 2 channels reveal the mechanisms for sudden cardiac death and treatment. Sci Adv (2022)

Release Date

2022-08-03

Peptides

Ryanodine receptor 2: AJKL
Peptidyl-prolyl cis-trans isomerase FKBP1B: BCDE
Calmodulin-1: FGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
B

K
C

L
D

B
E

C
F

D
G

E
H

F
I

G
J

H
K

I
L

Membrane

We predict this structure to be a membrane protein.
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Ryanodine receptor 2

Peptidyl-prolyl cis-trans isomerase FKBP1B

Calmodulin-1

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