SMTL ID : 8vjk.1

Structure of mouse RyR1 (high-Ca2+/CFF/ATP dataset)

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.4956, C.4959, 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.8: 4 residues within 4Å: Chain F: C.4956, C.4959, 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.15: 4 residues within 4Å: Chain G: C.4956, C.4959, 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.23: 4 residues within 4Å: Chain H: C.4956, C.4959, 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

4 x CFF: CAFFEINE(Non-covalent)

CFF.2: 6 residues within 4Å: Chain A: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 3 PLIP interactions: 3 interactions with chain A pi-Stacking: A:W.4714, A:W.4714, A:W.4714 CFF.9: 6 residues within 4Å: Chain F: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 3 PLIP interactions: 3 interactions with chain F pi-Stacking: F:W.4714, F:W.4714, F:W.4714 CFF.16: 6 residues within 4Å: Chain G: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 3 PLIP interactions: 3 interactions with chain G pi-Stacking: G:W.4714, G:W.4714, G:W.4714 CFF.24: 6 residues within 4Å: Chain H: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 3 PLIP interactions: 3 interactions with chain H pi-Stacking: H:W.4714, H:W.4714, H:W.4714

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

ATP.3: 13 residues within 4Å: Chain A: K.4214, K.4217, R.4218, M.4952, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.4957, A:I.4958, A:T.4977, A:H.4981, A:L.4983 Salt bridges: A:K.4214, A:K.4214, A:K.4217, A:K.4217, A:K.4217, A:R.4218 ATP.5: 10 residues within 4Å: Chain A: W.883, R.898, E.918, Y.921, N.922, M.925, H.994, W.997, R.1021, N.1036 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.905, A:N.922, A:R.1021, A:R.1021, A:N.1036 Salt bridges: A:R.898, A:R.898 pi-Stacking: A:W.997, A:W.997 ATP.10: 13 residues within 4Å: Chain F: K.4214, K.4217, R.4218, M.4952, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:F.4957, F:I.4958, F:T.4977, F:H.4981, F:L.4983 Salt bridges: F:K.4214, F:K.4214, F:K.4217, F:K.4217, F:K.4217, F:R.4218 ATP.12: 10 residues within 4Å: Chain F: W.883, R.898, E.918, Y.921, N.922, M.925, H.994, W.997, R.1021, N.1036 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:H.905, F:N.922, F:R.1021, F:R.1021, F:N.1036 Salt bridges: F:R.898, F:R.898 pi-Stacking: F:W.997, F:W.997 ATP.17: 13 residues within 4Å: Chain G: K.4214, K.4217, R.4218, M.4952, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:F.4957, G:I.4958, G:T.4977, G:H.4981, G:L.4983 Salt bridges: G:K.4214, G:K.4214, G:K.4217, G:K.4217, G:K.4217, G:R.4218 ATP.19: 10 residues within 4Å: Chain G: W.883, R.898, E.918, Y.921, N.922, M.925, H.994, W.997, R.1021, N.1036 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:H.905, G:N.922, G:R.1021, G:R.1021, G:N.1036 Salt bridges: G:R.898, G:R.898 pi-Stacking: G:W.997, G:W.997 ATP.25: 13 residues within 4Å: Chain H: K.4214, K.4217, R.4218, M.4952, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:F.4957, H:I.4958, H:T.4977, H:H.4981, H:L.4983 Salt bridges: H:K.4214, H:K.4214, H:K.4217, H:K.4217, H:K.4217, H:R.4218 ATP.27: 10 residues within 4Å: Chain H: W.883, R.898, E.918, Y.921, N.922, M.925, H.994, W.997, R.1021, N.1036 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:H.905, H:N.922, H:R.1021, H:R.1021, H:N.1036 Salt bridges: H:R.898, H:R.898 pi-Stacking: H:W.997, H:W.997

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.3896, E.3970, T.4999, H.5001 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3896, A:E.3970, A:T.4999 CA.11: 4 residues within 4Å: Chain F: E.3896, E.3970, T.4999, H.5001 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3896, F:E.3970, F:T.4999 CA.18: 4 residues within 4Å: Chain G: E.3896, E.3970, T.4999, H.5001 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3896, G:E.3970, G:T.4999 CA.26: 4 residues within 4Å: Chain H: E.3896, E.3970, T.4999, H.5001 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3896, H:E.3970, H:T.4999

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

PCW.6: 11 residues within 4Å: Chain A: L.4848, Y.4849, V.4852, N.4855, F.4856, Y.4907, Y.4910, T.4917, F.4921 Chain H: Y.4628 Ligands: PCW.22 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.4848, A:Y.4849, A:V.4852, A:F.4856, A:F.4856, A:T.4917, A:F.4921, A:F.4921 Hydrogen bonds: A:Y.4907, A:Y.4907 PCW.7: 13 residues within 4Å: Chain A: W.4792, M.4796, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Chain F: V.4851, N.4855, F.4856 Ligands: PCW.13 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:Y.4802, A:F.4805, A:A.4808, A:A.4809, A:L.4812, F:V.4851, F:F.4856, F:F.4856 Hydrogen bonds: A:N.4803 PCW.13: 11 residues within 4Å: Chain A: Y.4628 Chain F: L.4848, Y.4849, V.4852, N.4855, F.4856, Y.4907, Y.4910, T.4917, F.4921 Ligands: PCW.7 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:L.4848, F:Y.4849, F:V.4852, F:F.4856, F:F.4856, F:T.4917, F:F.4921, F:F.4921 Hydrogen bonds: F:Y.4907, F:Y.4907 PCW.14: 13 residues within 4Å: Chain F: W.4792, M.4796, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Chain G: V.4851, N.4855, F.4856 Ligands: PCW.20 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:Y.4802, F:F.4805, F:A.4808, F:A.4809, F:L.4812, G:V.4851, G:F.4856, G:F.4856 Hydrogen bonds: F:N.4803 PCW.20: 11 residues within 4Å: Chain F: Y.4628 Chain G: L.4848, Y.4849, V.4852, N.4855, F.4856, Y.4907, Y.4910, T.4917, F.4921 Ligands: PCW.14 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:L.4848, G:Y.4849, G:V.4852, G:F.4856, G:F.4856, G:T.4917, G:F.4921, G:F.4921 Hydrogen bonds: G:Y.4907, G:Y.4907 PCW.21: 13 residues within 4Å: Chain G: W.4792, M.4796, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Chain H: V.4851, N.4855, F.4856 Ligands: PCW.28 9 PLIP interactions: 6 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:Y.4802, G:F.4805, G:A.4808, G:A.4809, G:L.4812, H:V.4851, H:F.4856, H:F.4856 Hydrogen bonds: G:N.4803 PCW.22: 13 residues within 4Å: Chain A: V.4851, N.4855, F.4856 Chain H: W.4792, M.4796, Y.4802, N.4803, F.4805, F.4806, A.4808, A.4809, L.4812 Ligands: PCW.6 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain H Hydrophobic interactions: A:V.4851, A:F.4856, A:F.4856, H:Y.4802, H:F.4805, H:A.4808, H:A.4809, H:L.4812 Hydrogen bonds: H:N.4803 PCW.28: 11 residues within 4Å: Chain G: Y.4628 Chain H: L.4848, Y.4849, V.4852, N.4855, F.4856, Y.4907, Y.4910, T.4917, F.4921 Ligands: PCW.21 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:L.4848, H:Y.4849, H:V.4852, H:F.4856, H:F.4856, H:T.4917, H:F.4921, H:F.4921 Hydrogen bonds: H:Y.4907, 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
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 1

Peptidyl-prolyl cis-trans isomerase FKBP1A

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