SMTL ID : 8vk4.1

Structure of mouse RyR1 in complex with S100A1 (high-Ca2+/CFF/ATP dataset)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-8-4-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain B: S.20, D.25, Y.27, K.28, L.29, S.30, E.33, E.69 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.25, B:D.25, B:D.25, B:E.33, B:E.33 CA.2: 7 residues within 4Å: Chain B: L.62, D.63, N.65, D.67, E.69, D.71, E.74 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.63, B:E.74 CA.3: 6 residues within 4Å: Chain C: S.20, D.25, Y.27, K.28, L.29, E.33 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:S.20, C:D.25, C:K.28, C:E.33 CA.4: 6 residues within 4Å: Chain C: L.62, D.63, N.65, D.67, E.69, E.74 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.63, C:D.67, C:E.69, C:E.74 CA.8: 3 residues within 4Å: Chain G: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3896, G:E.3896, G:E.3970, G:T.4999 CA.15: 3 residues within 4Å: Chain H: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.3896, H:E.3896, H:E.3970, H:T.4999 CA.22: 3 residues within 4Å: Chain I: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.3896, I:E.3896, I:E.3970, I:T.4999 CA.30: 3 residues within 4Å: Chain J: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.3896, J:E.3896, J:E.3970, J:T.4999 CA.33: 8 residues within 4Å: Chain K: S.20, D.25, Y.27, K.28, L.29, S.30, E.33, E.69 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.25, K:D.25, K:D.25, K:E.33, K:E.33 CA.34: 7 residues within 4Å: Chain K: L.62, D.63, N.65, D.67, E.69, D.71, E.74 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.63, K:E.74 CA.35: 6 residues within 4Å: Chain L: S.20, D.25, Y.27, K.28, L.29, E.33 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:S.20, L:D.25, L:K.28, L:E.33 CA.36: 6 residues within 4Å: Chain L: L.62, D.63, N.65, D.67, E.69, E.74 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.63, L:D.67, L:E.69, L:E.74 CA.37: 6 residues within 4Å: Chain M: S.20, D.25, Y.27, K.28, L.29, E.33 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:S.20, M:D.25, M:K.28, M:E.33 CA.38: 6 residues within 4Å: Chain M: L.62, D.63, N.65, D.67, E.69, E.74 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.63, M:D.67, M:E.69, M:E.74 CA.39: 8 residues within 4Å: Chain N: S.20, D.25, Y.27, K.28, L.29, S.30, E.33, E.69 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:D.25, N:D.25, N:D.25, N:E.33, N:E.33 CA.40: 7 residues within 4Å: Chain N: L.62, D.63, N.65, D.67, E.69, D.71, E.74 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.63, N:E.74 CA.41: 8 residues within 4Å: Chain O: S.20, D.25, Y.27, K.28, L.29, S.30, E.33, E.69 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:D.25, O:D.25, O:D.25, O:E.33, O:E.33 CA.42: 7 residues within 4Å: Chain O: L.62, D.63, N.65, D.67, E.69, D.71, E.74 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.63, O:E.74 CA.43: 6 residues within 4Å: Chain P: S.20, D.25, Y.27, K.28, L.29, E.33 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:S.20, P:D.25, P:K.28, P:E.33 CA.44: 6 residues within 4Å: Chain P: L.62, D.63, N.65, D.67, E.69, E.74 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:D.63, P:D.67, P:E.69, P:E.74

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain G: C.4956, 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.12: 5 residues within 4Å: Chain H: C.4956, 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 ZN.19: 5 residues within 4Å: Chain I: C.4956, C.4959, F.4966, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.4956, I:C.4959, I:H.4976, I:H.4981 ZN.27: 5 residues within 4Å: Chain J: C.4956, C.4959, F.4966, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4956, J:C.4959, J:H.4976, J:H.4981

4 x CFF: CAFFEINE(Non-covalent)

CFF.6: 5 residues within 4Å: Chain G: 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.13: 5 residues within 4Å: Chain H: 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 CFF.20: 5 residues within 4Å: Chain I: E.4242, I.4245, W.4714, I.4994, W.5009 3 PLIP interactions: 3 interactions with chain I pi-Stacking: I:W.4714, I:W.4714, I:W.4714 CFF.28: 5 residues within 4Å: Chain J: E.4242, I.4245, W.4714, I.4994, W.5009 3 PLIP interactions: 3 interactions with chain J pi-Stacking: J:W.4714, J:W.4714, J:W.4714

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

ATP.7: 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 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:K.4214, 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.9: 12 residues within 4Å: Chain G: W.883, R.887, R.898, H.905, E.918, N.922, M.925, H.994, W.997, N.1019, R.1021, N.1036 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:N.922, G:R.1021, G:R.1021, G:N.1036 Salt bridges: G:R.887, G:R.898, G:R.898, G:H.905 pi-Stacking: G:W.997, G:W.997, G:W.997, G:W.997 ATP.14: 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 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:K.4214, 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.16: 12 residues within 4Å: Chain H: W.883, R.887, R.898, H.905, E.918, N.922, M.925, H.994, W.997, N.1019, R.1021, N.1036 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:N.922, H:R.1021, H:R.1021, H:N.1036 Salt bridges: H:R.887, H:R.898, H:R.898, H:H.905 pi-Stacking: H:W.997, H:W.997, H:W.997, H:W.997 ATP.21: 13 residues within 4Å: Chain I: 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 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:K.4214, I:F.4957, I:I.4958, I:T.4977, I:H.4981, I:L.4983 Salt bridges: I:K.4214, I:K.4214, I:K.4217, I:K.4217, I:K.4217, I:R.4218 ATP.23: 12 residues within 4Å: Chain I: W.883, R.887, R.898, H.905, E.918, N.922, M.925, H.994, W.997, N.1019, R.1021, N.1036 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:N.922, I:R.1021, I:R.1021, I:N.1036 Salt bridges: I:R.887, I:R.898, I:R.898, I:H.905 pi-Stacking: I:W.997, I:W.997, I:W.997, I:W.997 ATP.29: 13 residues within 4Å: Chain J: 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 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:K.4214, J:F.4957, J:I.4958, J:T.4977, J:H.4981, J:L.4983 Salt bridges: J:K.4214, J:K.4214, J:K.4217, J:K.4217, J:K.4217, J:R.4218 ATP.31: 12 residues within 4Å: Chain J: W.883, R.887, R.898, H.905, E.918, N.922, M.925, H.994, W.997, N.1019, R.1021, N.1036 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:N.922, J:R.1021, J:R.1021, J:N.1036 Salt bridges: J:R.887, J:R.898, J:R.898, J:H.905 pi-Stacking: J:W.997, J:W.997, J:W.997, J:W.997

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

PCW.10: 12 residues within 4Å: Chain G: L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, T.4917, F.4921 Chain J: Y.4628 Ligands: PCW.26 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:L.4848, G:Y.4849, G:Y.4849, G:V.4852, G:V.4852, G:F.4856, G:F.4856, G:T.4917, G:F.4921 Hydrogen bonds: G:Y.4907, G:Y.4907 PCW.11: 11 residues within 4Å: Chain G: W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, L.4812 Chain H: N.4855, F.4856 Ligands: PCW.17 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:L.4799, G:L.4799, G:F.4805, G:F.4806, G:F.4806, G:L.4812, H:F.4856, H:F.4856 Hydrogen bonds: G:N.4803 PCW.17: 12 residues within 4Å: Chain G: Y.4628 Chain H: L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, T.4917, F.4921 Ligands: PCW.11 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:L.4848, H:Y.4849, H:Y.4849, H:V.4852, H:V.4852, H:F.4856, H:F.4856, H:T.4917, H:F.4921 Hydrogen bonds: H:Y.4907, H:Y.4907 PCW.18: 11 residues within 4Å: Chain H: W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, L.4812 Chain I: N.4855, F.4856 Ligands: PCW.24 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:L.4799, H:L.4799, H:F.4805, H:F.4806, H:F.4806, H:L.4812, I:F.4856, I:F.4856 Hydrogen bonds: H:N.4803 PCW.24: 12 residues within 4Å: Chain H: Y.4628 Chain I: L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, T.4917, F.4921 Ligands: PCW.18 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:L.4848, I:Y.4849, I:Y.4849, I:V.4852, I:V.4852, I:F.4856, I:F.4856, I:T.4917, I:F.4921 Hydrogen bonds: I:Y.4907, I:Y.4907 PCW.25: 11 residues within 4Å: Chain I: W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, L.4812 Chain J: N.4855, F.4856 Ligands: PCW.32 9 PLIP interactions: 2 interactions with chain J, 7 interactions with chain I Hydrophobic interactions: J:F.4856, J:F.4856, I:L.4799, I:L.4799, I:F.4805, I:F.4806, I:F.4806, I:L.4812 Hydrogen bonds: I:N.4803 PCW.26: 11 residues within 4Å: Chain G: N.4855, F.4856 Chain J: W.4792, M.4796, L.4799, Y.4802, N.4803, F.4805, F.4806, L.4812 Ligands: PCW.10 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain G Hydrophobic interactions: J:L.4799, J:L.4799, J:F.4805, J:F.4806, J:F.4806, J:L.4812, G:F.4856, G:F.4856 Hydrogen bonds: J:N.4803 PCW.32: 12 residues within 4Å: Chain I: Y.4628 Chain J: L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, T.4917, F.4921 Ligands: PCW.25 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:L.4848, J:Y.4849, J:Y.4849, J:V.4852, J:V.4852, J:F.4856, J:F.4856, J:T.4917, J:F.4921 Hydrogen bonds: J:Y.4907, J:Y.4907

Links

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Citation

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

Release Date

2024-02-07

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1A: ADEF
Protein S100A1: BCKLMNOP
Ryanodine receptor 1: GHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

D
F

E
G

F
H

B
I

C
J

K
K

L
L

M
N

N
M

O
O

P
P

G
D

H
A

I
B

J
C

Membrane

We predict this structure to be a membrane protein.
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Peptidyl-prolyl cis-trans isomerase FKBP1A

Protein S100A1

Ryanodine receptor 1

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