SMTL ID : 8vjj.1

Structure of mouse RyR1 (EGTA-only dataset)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.4956, I.4958, C.4959, F.4966, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4956, A:C.4959, A:H.4976, A:H.4981 ZN.5: 6 residues within 4Å: Chain F: C.4956, I.4958, C.4959, F.4966, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4956, F:C.4959, F:H.4976, F:H.4981 ZN.7: 6 residues within 4Å: Chain G: C.4956, I.4958, C.4959, F.4966, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4956, G:C.4959, G:H.4976, G:H.4981 ZN.11: 6 residues within 4Å: Chain H: C.4956, I.4958, C.4959, F.4966, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4956, H:C.4959, H:H.4976, H:H.4981

8 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.2: 19 residues within 4Å: Chain A: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, R.4858, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Chain F: Y.4628, N.4803, F.4806, L.4812 Ligands: PCW.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.4848, A:Y.4849, A:F.4856, A:F.4856, A:Y.4910, A:Y.4910, A:T.4917, A:F.4921 Hydrogen bonds: A:Y.4907 PCW.3: 17 residues within 4Å: Chain A: Y.4789, W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Chain G: L.4848, V.4851, V.4852, N.4855, F.4856 Ligands: PCW.8 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:W.4792, A:W.4792, A:F.4805, A:F.4806, A:L.4812, G:L.4848, G:V.4851 Hydrogen bonds: A:N.4803 PCW.4: 17 residues within 4Å: Chain A: L.4848, V.4851, V.4852, N.4855, F.4856 Chain F: Y.4789, W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Ligands: PCW.2 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:W.4792, F:F.4805, F:F.4806, F:F.4806, F:L.4812, A:V.4851 Hydrogen bonds: F:N.4803 PCW.6: 19 residues within 4Å: Chain F: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, R.4858, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Chain H: Y.4628, N.4803, F.4806, L.4812 Ligands: PCW.10 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:L.4848, F:Y.4849, F:F.4856, F:F.4856, F:F.4856, F:Y.4910, F:Y.4910, F:T.4917, F:F.4921 Hydrogen bonds: F:Y.4907 PCW.8: 19 residues within 4Å: Chain A: Y.4628, N.4803, F.4806, L.4812 Chain G: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, R.4858, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Ligands: PCW.3 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:L.4848, G:L.4848, G:Y.4849, G:F.4856, G:F.4856, G:Y.4907, G:Y.4910, G:Y.4910, G:T.4917, G:F.4921, G:F.4921 Hydrogen bonds: G:Y.4907 PCW.9: 17 residues within 4Å: Chain G: Y.4789, W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Chain H: L.4848, V.4851, V.4852, N.4855, F.4856 Ligands: PCW.12 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:W.4792, G:F.4805, G:F.4806, G:L.4812, H:V.4851, H:F.4856 Hydrogen bonds: G:N.4803 PCW.10: 17 residues within 4Å: Chain F: L.4848, V.4851, V.4852, N.4855, F.4856 Chain H: Y.4789, W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Ligands: PCW.6 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain F Hydrophobic interactions: H:W.4792, H:F.4805, H:L.4812, F:L.4848 Hydrogen bonds: H:N.4803 PCW.12: 19 residues within 4Å: Chain G: Y.4628, N.4803, F.4806, L.4812 Chain H: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, R.4858, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Ligands: PCW.9 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:L.4848, H:Y.4849, H:F.4856, H:F.4856, H:F.4856, H:Y.4910, H:Y.4910, H:T.4917, H:F.4921 Hydrogen bonds: H:Y.4907

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weninger, G. et al., Structural insights into the regulation of RyR1 by S100A1. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-01-17

Peptides

Ryanodine receptor 1: AFGH
Peptidyl-prolyl cis-trans isomerase FKBP1A: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
D

G
B

H
C

B
E

C
H

D
F

E
G

Membrane

We predict this structure to be a membrane protein.
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Ryanodine receptor 1

Peptidyl-prolyl cis-trans isomerase FKBP1A

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