SMTL ID : 8uxm.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.21, D.23, G.24, D.25, G.26, T.27, E.32 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.21, A:D.23, A:D.23, A:D.25, A:T.27 CA.2: 6 residues within 4Å: Chain A: D.57, D.59, G.60, N.61, T.63, E.68 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.57, A:D.59, A:E.68, A:E.68 CA.3: 8 residues within 4Å: Chain A: F.93, D.94, K.95, D.96, Y.100, I.101, S.102, E.105 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:D.96, A:E.105 CA.4: 6 residues within 4Å: Chain A: D.130, D.134, Q.136, V.137, N.138, E.141 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.130, A:D.130, A:D.134, A:Q.136 CA.7: 3 residues within 4Å: Chain B: E.3848, E.3922, T.4931 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.3848, B:E.3848, B:E.3922, B:T.4931 CA.9: 7 residues within 4Å: Chain G: D.21, D.23, G.24, D.25, G.26, T.27, E.32 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.21, G:D.23, G:D.23, G:D.25, G:T.27 CA.10: 6 residues within 4Å: Chain G: D.57, D.59, G.60, N.61, T.63, E.68 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.57, G:D.59, G:E.68, G:E.68 CA.11: 8 residues within 4Å: Chain G: F.93, D.94, K.95, D.96, Y.100, I.101, S.102, E.105 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.94, G:D.96, G:E.105 CA.12: 6 residues within 4Å: Chain G: D.130, D.134, Q.136, V.137, N.138, E.141 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.130, G:D.130, G:D.134, G:Q.136 CA.13: 7 residues within 4Å: Chain H: D.21, D.23, G.24, D.25, G.26, T.27, E.32 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.21, H:D.23, H:D.23, H:D.25, H:T.27 CA.14: 6 residues within 4Å: Chain H: D.57, D.59, G.60, N.61, T.63, E.68 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.57, H:D.59, H:E.68, H:E.68 CA.15: 8 residues within 4Å: Chain H: F.93, D.94, K.95, D.96, Y.100, I.101, S.102, E.105 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.94, H:D.96, H:E.105 CA.16: 6 residues within 4Å: Chain H: D.130, D.134, Q.136, V.137, N.138, E.141 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.130, H:D.130, H:D.134, H:Q.136 CA.17: 7 residues within 4Å: Chain I: D.21, D.23, G.24, D.25, G.26, T.27, E.32 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.21, I:D.23, I:D.23, I:D.25, I:T.27 CA.18: 6 residues within 4Å: Chain I: D.57, D.59, G.60, N.61, T.63, E.68 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.57, I:D.59, I:E.68, I:E.68 CA.19: 8 residues within 4Å: Chain I: F.93, D.94, K.95, D.96, Y.100, I.101, S.102, E.105 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.94, I:D.96, I:E.105 CA.20: 6 residues within 4Å: Chain I: D.130, D.134, Q.136, V.137, N.138, E.141 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.130, I:D.130, I:D.134, I:Q.136 CA.23: 3 residues within 4Å: Chain J: E.3848, E.3922, T.4931 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.3848, J:E.3848, J:E.3922, J:T.4931 CA.27: 3 residues within 4Å: Chain K: E.3848, E.3922, T.4931 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.3848, K:E.3848, K:E.3922, K:T.4931 CA.31: 3 residues within 4Å: Chain L: E.3848, E.3922, T.4931 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.3848, L:E.3848, L:E.3922, L:T.4931

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain B: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4888, B:C.4891, B:H.4908, B:H.4913 ZN.21: 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.25: 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.29: 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.6: 13 residues within 4Å: Chain B: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.4885, B:F.4889, B:I.4890, B:T.4909, B:T.4909, B:N.4914, B:L.4915 Salt bridges: B:K.4169, B:R.4170 ATP.8: 2 residues within 4Å: Chain B: H.915, R.1031 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.1031 ATP.22: 13 residues within 4Å: Chain J: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:E.4885, J:F.4889, J:I.4890, J:T.4909, J:T.4909, J:N.4914, J:L.4915 Salt bridges: J:K.4169, J:R.4170 ATP.24: 2 residues within 4Å: Chain J: H.915, R.1031 1 PLIP interactions: 1 interactions with chain J Salt bridges: J:R.1031 ATP.26: 13 residues within 4Å: Chain K: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:E.4885, K:F.4889, K:I.4890, K:T.4909, K:T.4909, K:N.4914, K:L.4915 Salt bridges: K:K.4169, K:R.4170 ATP.28: 2 residues within 4Å: Chain K: H.915, R.1031 1 PLIP interactions: 1 interactions with chain K Salt bridges: K:R.1031 ATP.30: 13 residues within 4Å: Chain L: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, I.4890, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:E.4885, L:F.4889, L:I.4890, L:T.4909, L:T.4909, L:N.4914, L:L.4915 Salt bridges: L:K.4169, L:R.4170 ATP.32: 2 residues within 4Å: Chain L: H.915, R.1031 1 PLIP interactions: 1 interactions with chain L Salt bridges: L:R.1031

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

Calmodulin-1: AGHI
Ryanodine receptor 2: BJKL
Peptidyl-prolyl cis-trans isomerase FKBP1B: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

G
J

H
L

I
K

B
A

J
B

K
C

L
D

C
E

D
F

E
G

F
H

Calmodulin-1

Ryanodine receptor 2

Peptidyl-prolyl cis-trans isomerase FKBP1B

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