SMTL ID : 8rru.1

Structure of RyR1 reconstituted into lipid liposomes in primed 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 E: C.4948, C.4951, H.4968, H.4973 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.4948, E:H.4968, E:H.4973 ZN.5: 4 residues within 4Å: Chain F: C.4948, C.4951, H.4968, H.4973 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.4948, F:H.4968, F:H.4973 ZN.9: 4 residues within 4Å: Chain G: C.4948, C.4951, H.4968, H.4973 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.4948, G:H.4968, G:H.4973 ZN.13: 4 residues within 4Å: Chain H: C.4948, C.4951, H.4968, H.4973 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.4948, H:H.4968, H:H.4973

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

ATP.2: 10 residues within 4Å: Chain E: K.4201, K.4204, R.4205, M.4944, C.4948, F.4949, T.4969, H.4973, N.4974, L.4975 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:H.4973, E:L.4975 Salt bridges: E:K.4201, E:K.4204, E:K.4204, E:K.4204, E:R.4205 ATP.6: 10 residues within 4Å: Chain F: K.4201, K.4204, R.4205, M.4944, C.4948, F.4949, T.4969, H.4973, N.4974, L.4975 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:H.4973, F:L.4975 Salt bridges: F:K.4201, F:K.4204, F:K.4204, F:K.4204, F:R.4205 ATP.10: 10 residues within 4Å: Chain G: K.4201, K.4204, R.4205, M.4944, C.4948, F.4949, T.4969, H.4973, N.4974, L.4975 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:H.4973, G:L.4975 Salt bridges: G:K.4201, G:K.4204, G:K.4204, G:K.4204, G:R.4205 ATP.14: 10 residues within 4Å: Chain H: K.4201, K.4204, R.4205, M.4944, C.4948, F.4949, T.4969, H.4973, N.4974, L.4975 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:H.4973, H:L.4975 Salt bridges: H:K.4201, H:K.4204, H:K.4204, H:K.4204, H:R.4205

4 x CFF: CAFFEINE(Non-covalent)

CFF.3: 5 residues within 4Å: Chain E: Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.4236, E:Y.5004 pi-Stacking: E:W.4706, E:W.4706, E:W.4706 CFF.7: 5 residues within 4Å: Chain F: Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.4236, F:Y.5004 pi-Stacking: F:W.4706, F:W.4706, F:W.4706 CFF.11: 5 residues within 4Å: Chain G: Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Q.4236, G:Y.5004 pi-Stacking: G:W.4706, G:W.4706, G:W.4706 CFF.15: 5 residues within 4Å: Chain H: Q.4236, W.4706, I.4986, W.5001, Y.5004 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Q.4236, H:Y.5004 pi-Stacking: H:W.4706, H:W.4706, H:W.4706

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain E: E.3883, E.3957, Q.3960, T.4991 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.3883, E:E.3957, E:T.4991 CA.8: 4 residues within 4Å: Chain F: E.3883, E.3957, Q.3960, T.4991 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3883, F:E.3957, F:T.4991 CA.12: 4 residues within 4Å: Chain G: E.3883, E.3957, Q.3960, T.4991 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3883, G:E.3957, G:T.4991 CA.16: 4 residues within 4Å: Chain H: E.3883, E.3957, Q.3960, T.4991 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3883, H:E.3957, H: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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
H

D
I

E
B

F
E

G
G

H
J

I
C

J
F

K
K

L
M

Membrane

We predict this structure to be a membrane protein.
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Peptidyl-prolyl cis-trans isomerase FKBP1B

Ryanodine receptor 1

Nanobody 9657

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