SMTL ID : 8vk3.1

Structure of mouse RyR1 in complex with S100A1 (EGTA-only dataset)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-8-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.5: 4 residues within 4Å: Chain N: C.4956, C.4959, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.4956, N:C.4959, N:H.4976, N:H.4981 ZN.7: 4 residues within 4Å: Chain O: C.4956, C.4959, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.4956, O:C.4959, O:H.4976, O:H.4981 ZN.11: 4 residues within 4Å: Chain P: C.4956, C.4959, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.4956, P:C.4959, P:H.4976, P:H.4981

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

PCW.2: 9 residues within 4Å: Chain A: L.4848, Y.4849, N.4855, F.4856, Y.4907, Y.4910, F.4921 Chain N: Y.4628 Ligands: PCW.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.4848, A:Y.4849, A:Y.4849, A:Y.4849, A:F.4856, A:F.4856, A:F.4856, A:Y.4907, A:Y.4910, A:Y.4910, A:F.4921 Hydrogen bonds: A:Y.4907, A:Y.4907 PCW.3: 9 residues within 4Å: Chain A: W.4792, Y.4802, N.4803, F.4805, F.4806 Chain O: L.4848, N.4855, F.4856 Ligands: PCW.8 8 PLIP interactions: 2 interactions with chain O, 6 interactions with chain A Hydrophobic interactions: O:L.4848, O:F.4856, A:W.4792, A:Y.4802, A:F.4805, A:F.4806, A:F.4806 Hydrogen bonds: A:N.4803 PCW.4: 9 residues within 4Å: Chain A: L.4848, N.4855, F.4856 Chain N: W.4792, Y.4802, N.4803, F.4805, F.4806 Ligands: PCW.2 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain N Hydrophobic interactions: A:L.4848, A:F.4856, N:W.4792, N:F.4805, N:F.4806, N:F.4806 Hydrogen bonds: N:N.4803 PCW.6: 9 residues within 4Å: Chain N: L.4848, Y.4849, N.4855, F.4856, Y.4907, Y.4910, F.4921 Chain P: Y.4628 Ligands: PCW.10 13 PLIP interactions: 13 interactions with chain N Hydrophobic interactions: N:L.4848, N:Y.4849, N:Y.4849, N:Y.4849, N:F.4856, N:F.4856, N:F.4856, N:Y.4907, N:Y.4910, N:Y.4910, N:F.4921 Hydrogen bonds: N:Y.4907, N:Y.4907 PCW.8: 9 residues within 4Å: Chain A: Y.4628 Chain O: L.4848, Y.4849, N.4855, F.4856, Y.4907, Y.4910, F.4921 Ligands: PCW.3 13 PLIP interactions: 13 interactions with chain O Hydrophobic interactions: O:L.4848, O:Y.4849, O:Y.4849, O:Y.4849, O:F.4856, O:F.4856, O:F.4856, O:Y.4907, O:Y.4910, O:Y.4910, O:F.4921 Hydrogen bonds: O:Y.4907, O:Y.4907 PCW.9: 10 residues within 4Å: Chain O: W.4792, Y.4802, N.4803, F.4805, F.4806, A.4808 Chain P: L.4848, N.4855, F.4856 Ligands: PCW.12 9 PLIP interactions: 7 interactions with chain O, 2 interactions with chain P Hydrophobic interactions: O:W.4792, O:Y.4802, O:F.4805, O:F.4806, O:F.4806, O:A.4808, P:L.4848, P:F.4856 Hydrogen bonds: O:N.4803 PCW.10: 10 residues within 4Å: Chain N: L.4848, N.4855, F.4856 Chain P: W.4792, Y.4802, N.4803, F.4805, F.4806, A.4808 Ligands: PCW.6 9 PLIP interactions: 2 interactions with chain N, 7 interactions with chain P Hydrophobic interactions: N:L.4848, N:F.4856, P:W.4792, P:Y.4802, P:F.4805, P:F.4806, P:F.4806, P:A.4808 Hydrogen bonds: P:N.4803 PCW.12: 9 residues within 4Å: Chain O: Y.4628 Chain P: L.4848, Y.4849, N.4855, F.4856, Y.4907, Y.4910, F.4921 Ligands: PCW.9 13 PLIP interactions: 13 interactions with chain P Hydrophobic interactions: P:L.4848, P:Y.4849, P:Y.4849, P:Y.4849, P:F.4856, P:F.4856, P:F.4856, P:Y.4907, P:Y.4910, P:Y.4910, P:F.4921 Hydrogen bonds: P:Y.4907, P: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

2024-01-24

Peptides

Ryanodine receptor 1: ANOP
Peptidyl-prolyl cis-trans isomerase FKBP1A: BEFG
Protein S100A1: CDHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
D

O
B

P
C

B
E

E
H

F
F

G
G

C
J

D
I

H
K

I
M

J
O

K
L

L
N

M
P

Membrane

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

Peptidyl-prolyl cis-trans isomerase FKBP1A

Protein S100A1

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