SMTL ID : 8uxe.1

Structure of PKA phosphorylated human RyR2-R420Q in the closed state in the presence of ARM210

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain E: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4888, E:C.4891, E:H.4908, E:H.4913 ZN.5: 4 residues within 4Å: Chain F: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4888, F:C.4891, F:H.4908, F:H.4913 ZN.9: 4 residues within 4Å: Chain G: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4888, G:C.4891, G:H.4908, G:H.4913 ZN.13: 4 residues within 4Å: Chain H: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4888, H:C.4891, H:H.4908, H:H.4913

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

ATP.2: 11 residues within 4Å: Chain E: K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:F.4889, E:I.4890, E:T.4909, E:L.4915 Salt bridges: E:K.4166, E:K.4169, E:K.4169, E:K.4169, E:R.4170 ATP.3: 10 residues within 4Å: Chain E: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029 Ligands: KVR.4 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:Y.931, E:N.932, E:Q.1014, E:W.1016, E:Q.1022, E:N.1029 Salt bridges: E:R.1011, E:R.1011, E:R.1011 ATP.6: 11 residues within 4Å: Chain F: K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:F.4889, F:I.4890, F:T.4909, F:L.4915 Salt bridges: F:K.4166, F:K.4169, F:K.4169, F:K.4169, F:R.4170 ATP.7: 10 residues within 4Å: Chain F: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029 Ligands: KVR.8 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:Y.931, F:N.932, F:Q.1014, F:W.1016, F:Q.1022, F:N.1029 Salt bridges: F:R.1011, F:R.1011, F:R.1011 ATP.10: 11 residues within 4Å: Chain G: K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:F.4889, G:I.4890, G:T.4909, G:L.4915 Salt bridges: G:K.4166, G:K.4169, G:K.4169, G:K.4169, G:R.4170 ATP.11: 10 residues within 4Å: Chain G: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029 Ligands: KVR.12 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:Y.931, G:N.932, G:Q.1014, G:W.1016, G:Q.1022, G:N.1029 Salt bridges: G:R.1011, G:R.1011, G:R.1011 ATP.14: 11 residues within 4Å: Chain H: K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:F.4889, H:I.4890, H:T.4909, H:L.4915 Salt bridges: H:K.4166, H:K.4169, H:K.4169, H:K.4169, H:R.4170 ATP.15: 10 residues within 4Å: Chain H: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029 Ligands: KVR.16 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:Y.931, H:N.932, H:Q.1014, H:W.1016, H:Q.1022, H:N.1029 Salt bridges: H:R.1011, H:R.1011, H:R.1011

4 x KVR: 4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benzoic acid(Non-covalent)

KVR.4: 10 residues within 4Å: Chain E: W.893, M.935, W.1007, R.1031, R.1041, T.1042, S.1045, N.1046, S.1049 Ligands: ATP.3 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:T.1042 Salt bridges: E:R.1031, E:R.1041 pi-Stacking: E:W.893, E:W.893 KVR.8: 10 residues within 4Å: Chain F: W.893, M.935, W.1007, R.1031, R.1041, T.1042, S.1045, N.1046, S.1049 Ligands: ATP.7 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:T.1042 Salt bridges: F:R.1031, F:R.1041 pi-Stacking: F:W.893, F:W.893 KVR.12: 10 residues within 4Å: Chain G: W.893, M.935, W.1007, R.1031, R.1041, T.1042, S.1045, N.1046, S.1049 Ligands: ATP.11 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:T.1042 Salt bridges: G:R.1031, G:R.1041 pi-Stacking: G:W.893, G:W.893 KVR.16: 10 residues within 4Å: Chain H: W.893, M.935, W.1007, R.1031, R.1041, T.1042, S.1045, N.1046, S.1049 Ligands: ATP.15 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:T.1042 Salt bridges: H:R.1031, H:R.1041 pi-Stacking: H:W.893, H:W.893

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miotto, M.C. et al., Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders. Nat Commun (2024)

Release Date

2023-11-22

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1B: ABCD
Ryanodine receptor 2: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
A

F
B

G
C

H
D

Membrane

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

Ryanodine receptor 2

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