SMTL ID : 8uxi.1

Structure of PKA phosphorylated human RyR2-R420W in the open state in the presence of calcium

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 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.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: 12 residues within 4Å: Chain A: K.4169, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.4885, A:F.4889, A:H.4913, A:L.4915 Salt bridges: A:K.4169 ATP.4: 6 residues within 4Å: Chain A: K.897, E.928, N.932, W.1007, R.1011, R.1031 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.932, A:W.1007, A:W.1007, A:R.1011 Salt bridges: A:R.1011, A:R.1031 ATP.6: 12 residues within 4Å: Chain F: K.4169, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.4885, F:F.4889, F:H.4913, F:L.4915 Salt bridges: F:K.4169 ATP.8: 6 residues within 4Å: Chain F: K.897, E.928, N.932, W.1007, R.1011, R.1031 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.932, F:W.1007, F:W.1007, F:R.1011 Salt bridges: F:R.1011, F:R.1031 ATP.10: 12 residues within 4Å: Chain G: K.4169, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:E.4885, G:F.4889, G:H.4913, G:L.4915 Salt bridges: G:K.4169 ATP.12: 6 residues within 4Å: Chain G: K.897, E.928, N.932, W.1007, R.1011, R.1031 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:N.932, G:W.1007, G:W.1007, G:R.1011 Salt bridges: G:R.1011, G:R.1031 ATP.14: 12 residues within 4Å: Chain H: K.4169, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:E.4885, H:F.4889, H:H.4913, H:L.4915 Salt bridges: H:K.4169 ATP.16: 6 residues within 4Å: Chain H: K.897, E.928, N.932, W.1007, R.1011, R.1031 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:N.932, H:W.1007, H:W.1007, H:R.1011 Salt bridges: H:R.1011, H:R.1031

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3848, A:E.3922, A:T.4931 CA.7: 4 residues within 4Å: Chain F: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3848, F:E.3922, F:T.4931 CA.11: 4 residues within 4Å: Chain G: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3848, G:E.3922, G:T.4931 CA.15: 4 residues within 4Å: Chain H: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3848, H:E.3922, H:T.4931

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

Ryanodine receptor 2: AFGH
Peptidyl-prolyl cis-trans isomerase FKBP1B: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

G
C

H
D

B
E

C
F

D
G

E
H

Membrane

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

Peptidyl-prolyl cis-trans isomerase FKBP1B

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