SMTL ID : 8rrt.1

Structure of rabbit RyR1 reconstituted into lipid liposomes in open state in complex with FKBP and Nb9657

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4948, A:C.4951, A:H.4968, A:H.4973 ZN.5: 4 residues within 4Å: Chain B: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4948, B:C.4951, B:H.4968, B:H.4973 ZN.9: 4 residues within 4Å: Chain C: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4948, C:C.4951, C:H.4968, C:H.4973 ZN.13: 4 residues within 4Å: Chain D: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.4948, D:C.4951, D:H.4968, D:H.4973

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

ATP.2: 11 residues within 4Å: Chain A: R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, L.4975 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.4949, A:H.4973, A:L.4975 Salt bridges: A:R.4205 ATP.6: 11 residues within 4Å: Chain B: R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, L.4975 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.4949, B:H.4973, B:L.4975 Salt bridges: B:R.4205 ATP.10: 11 residues within 4Å: Chain C: R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, L.4975 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.4949, C:H.4973, C:L.4975 Salt bridges: C:R.4205 ATP.14: 11 residues within 4Å: Chain D: R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, L.4975 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:F.4949, D:H.4973, D:L.4975 Salt bridges: D:R.4205

4 x CFF: CAFFEINE(Non-covalent)

CFF.3: 4 residues within 4Å: Chain A: E.4229, W.4706, I.4986, Y.5004 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.5004 pi-Stacking: A:W.4706, A:W.4706, A:W.4706 CFF.7: 4 residues within 4Å: Chain B: E.4229, W.4706, I.4986, Y.5004 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.5004 pi-Stacking: B:W.4706, B:W.4706, B:W.4706 CFF.11: 4 residues within 4Å: Chain C: E.4229, W.4706, I.4986, Y.5004 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.5004 pi-Stacking: C:W.4706, C:W.4706, C:W.4706 CFF.15: 4 residues within 4Å: Chain D: E.4229, W.4706, I.4986, Y.5004 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.5004 pi-Stacking: D:W.4706, D:W.4706, D:W.4706

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.3883, E.3957, T.4991 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.3883, A:T.4991 CA.8: 3 residues within 4Å: Chain B: E.3883, E.3957, T.4991 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.3883, B:T.4991 CA.12: 3 residues within 4Å: Chain C: E.3883, E.3957, T.4991 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.3883, C:T.4991 CA.16: 3 residues within 4Å: Chain D: E.3883, E.3957, T.4991 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.3883, D:T.4991

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 1: ABCD
Peptidyl-prolyl cis-trans isomerase FKBP1B: EFGH
Nanobody 9657: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
G

D
J

E
A

F
D

G
H

H
I

I
C

J
F

K
K

L
M

Membrane

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

Peptidyl-prolyl cis-trans isomerase FKBP1B

Nanobody 9657

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