SMTL ID : 8rrs.1

Structure of mouse RyR2 solubilised in detergent in open state in complex with Ca2+, ATP, caffeine and Nb9657.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: K.4165, K.4168, R.4169, M.4883, K.4886, C.4887, F.4888, I.4889, F.4904, T.4908, H.4912, N.4913, L.4914 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.4888, A:T.4908, A:N.4913, A:L.4914 Salt bridges: A:K.4165, A:K.4168, A:K.4168, A:R.4169 ATP.5: 13 residues within 4Å: Chain C: K.4165, K.4168, R.4169, M.4883, K.4886, C.4887, F.4888, I.4889, F.4904, T.4908, H.4912, N.4913, L.4914 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:F.4888, C:T.4908, C:N.4913, C:L.4914 Salt bridges: C:K.4165, C:K.4168, C:K.4168, C:R.4169 ATP.9: 13 residues within 4Å: Chain E: K.4165, K.4168, R.4169, M.4883, K.4886, C.4887, F.4888, I.4889, F.4904, T.4908, H.4912, N.4913, L.4914 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:F.4888, E:T.4908, E:N.4913, E:L.4914 Salt bridges: E:K.4165, E:K.4168, E:K.4168, E:R.4169 ATP.13: 13 residues within 4Å: Chain F: K.4165, K.4168, R.4169, M.4883, K.4886, C.4887, F.4888, I.4889, F.4904, T.4908, H.4912, N.4913, L.4914 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:F.4888, F:T.4908, F:N.4913, F:L.4914 Salt bridges: F:K.4165, F:K.4168, F:K.4168, F:R.4169

4 x CFF: CAFFEINE(Non-covalent)

CFF.2: 7 residues within 4Å: Chain A: F.3713, E.4193, I.4196, W.4644, I.4925, W.4940, Y.4943 3 PLIP interactions: 3 interactions with chain A pi-Stacking: A:W.4644, A:W.4644, A:W.4644 CFF.6: 7 residues within 4Å: Chain C: F.3713, E.4193, I.4196, W.4644, I.4925, W.4940, Y.4943 3 PLIP interactions: 3 interactions with chain C pi-Stacking: C:W.4644, C:W.4644, C:W.4644 CFF.10: 7 residues within 4Å: Chain E: F.3713, E.4193, I.4196, W.4644, I.4925, W.4940, Y.4943 3 PLIP interactions: 3 interactions with chain E pi-Stacking: E:W.4644, E:W.4644, E:W.4644 CFF.14: 7 residues within 4Å: Chain F: F.3713, E.4193, I.4196, W.4644, I.4925, W.4940, Y.4943 3 PLIP interactions: 3 interactions with chain F pi-Stacking: F:W.4644, F:W.4644, F:W.4644

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.4887, C.4890, H.4907, H.4912 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4887, A:C.4890, A:H.4907, A:H.4912 ZN.7: 4 residues within 4Å: Chain C: C.4887, C.4890, H.4907, H.4912 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4887, C:C.4890, C:H.4907, C:H.4912 ZN.11: 4 residues within 4Å: Chain E: C.4887, C.4890, H.4907, H.4912 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4887, E:C.4890, E:H.4907, E:H.4912 ZN.15: 4 residues within 4Å: Chain F: C.4887, C.4890, H.4907, H.4912 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4887, F:C.4890, F:H.4907, F:H.4912

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.3847, E.3921, T.4930, H.4932 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3847, A:E.3921, A:T.4930 CA.8: 4 residues within 4Å: Chain C: E.3847, E.3921, T.4930, H.4932 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.3847, C:E.3921, C:T.4930 CA.12: 4 residues within 4Å: Chain E: E.3847, E.3921, T.4930, H.4932 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.3847, E:E.3921, E:T.4930 CA.16: 4 residues within 4Å: Chain F: E.3847, E.3921, T.4930, H.4932 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3847, F:E.3921, F:T.4930

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C. et al., Rapid small-scale nanobody-assisted purification of ryanodine receptors for cryo-EM. J.Biol.Chem. (2024)

Release Date

2024-10-09

Peptides

Ryanodine receptor 2: ACEF
Nanobody 9657: BDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

F
F

B
B

D
D

G
G

H
I

Membrane

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

Nanobody 9657

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