SMTL ID : 7ua9.1

Structure of dephosphorylated human RyR2 in the open state

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.6: 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.11: 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.16: 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: 14 residues within 4Å: Chain E: K.4166, 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 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:F.4889, E:H.4913, E:L.4915 Salt bridges: E:K.4166, E:K.4169, E:K.4169, E:K.4169, E:R.4170, E:R.4170, E:R.4170 ATP.5: 9 residues within 4Å: Chain E: K.897, R.908, H.915, C.917, E.928, W.1007, R.1011, W.1016, N.1029 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.908, E:H.915, E:W.1007, E:R.1011, E:N.1029 Salt bridges: E:R.1011 ATP.7: 14 residues within 4Å: Chain F: K.4166, 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 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:F.4889, F:H.4913, F:L.4915 Salt bridges: F:K.4166, F:K.4169, F:K.4169, F:K.4169, F:R.4170, F:R.4170, F:R.4170 ATP.10: 9 residues within 4Å: Chain F: K.897, R.908, H.915, C.917, E.928, W.1007, R.1011, W.1016, N.1029 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.908, F:H.915, F:W.1007, F:R.1011, F:N.1029 Salt bridges: F:R.1011 ATP.12: 14 residues within 4Å: Chain G: K.4166, 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 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:F.4889, G:H.4913, G:L.4915 Salt bridges: G:K.4166, G:K.4169, G:K.4169, G:K.4169, G:R.4170, G:R.4170, G:R.4170 ATP.15: 9 residues within 4Å: Chain G: K.897, R.908, H.915, C.917, E.928, W.1007, R.1011, W.1016, N.1029 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:R.908, G:H.915, G:W.1007, G:R.1011, G:N.1029 Salt bridges: G:R.1011 ATP.17: 14 residues within 4Å: Chain H: K.4166, 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 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:F.4889, H:H.4913, H:L.4915 Salt bridges: H:K.4166, H:K.4169, H:K.4169, H:K.4169, H:R.4170, H:R.4170, H:R.4170 ATP.20: 9 residues within 4Å: Chain H: K.897, R.908, H.915, C.917, E.928, W.1007, R.1011, W.1016, N.1029 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:R.908, H:H.915, H:W.1007, H:R.1011, H:N.1029 Salt bridges: H:R.1011

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain E: E.3848, E.3922, T.4931 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.3848, E:E.3848, E:E.3922, E:E.3922, E:T.4931 CA.8: 3 residues within 4Å: Chain F: E.3848, E.3922, T.4931 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.3848, F:E.3848, F:E.3922, F:E.3922, F:T.4931 CA.13: 3 residues within 4Å: Chain G: E.3848, E.3922, T.4931 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.3848, G:E.3848, G:E.3922, G:E.3922, G:T.4931 CA.18: 3 residues within 4Å: Chain H: E.3848, E.3922, T.4931 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.3848, H:E.3848, H:E.3922, H:E.3922, H:T.4931

4 x XAN: XANTHINE(Non-covalent)

XAN.4: 4 residues within 4Å: Chain E: W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.4944, E:Y.4944 pi-Stacking: E:W.4645, E:W.4645, E:W.4645 XAN.9: 4 residues within 4Å: Chain F: W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.4944, F:Y.4944 pi-Stacking: F:W.4645, F:W.4645, F:W.4645 XAN.14: 4 residues within 4Å: Chain G: W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Y.4944, G:Y.4944 pi-Stacking: G:W.4645, G:W.4645, G:W.4645 XAN.19: 4 residues within 4Å: Chain H: W.4645, I.4926, W.4941, Y.4944 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Y.4944, H:Y.4944 pi-Stacking: H:W.4645, H:W.4645, H: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

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

Peptidyl-prolyl cis-trans isomerase FKBP1B

Ryanodine receptor 2

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