SMTL ID : 8rrx.1

Structure of RyR1 reconstituted into lipid nanodisc in primed state in complex with Ca2+, ATP, caffeine 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 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.7: 4 residues within 4Å: Chain E: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4948, E:C.4951, E:H.4968, E:H.4973 ZN.11: 4 residues within 4Å: Chain H: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4948, H:C.4951, H:H.4968, H:H.4973 ZN.16: 4 residues within 4Å: Chain K: C.4948, C.4951, H.4968, H.4973 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.4948, K:C.4951, K:H.4968, K:H.4973

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 11 residues within 4Å: Chain B: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4902, F.4906, T.4909, F.4913 Chain E: Y.4620, F.4798 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:L.4840, B:Y.4841, B:F.4848, B:F.4848, B:F.4849, B:Y.4902, B:Y.4902, B:F.4906, B:T.4909, B:F.4913, E:F.4798 POV.6: 11 residues within 4Å: Chain E: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4902, F.4906, T.4909, F.4913 Chain H: Y.4620, F.4798 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:L.4840, E:Y.4841, E:F.4848, E:F.4848, E:F.4849, E:Y.4902, E:Y.4902, E:F.4906, E:T.4909, E:F.4913, H:F.4798 POV.12: 11 residues within 4Å: Chain H: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4902, F.4906, T.4909, F.4913 Chain K: Y.4620, F.4798 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain K Hydrophobic interactions: H:L.4840, H:Y.4841, H:F.4848, H:F.4848, H:F.4849, H:Y.4902, H:Y.4902, H:F.4906, H:T.4909, H:F.4913, K:F.4798 POV.17: 11 residues within 4Å: Chain B: Y.4620, F.4798 Chain K: L.4840, Y.4841, N.4847, F.4848, F.4849, Y.4902, F.4906, T.4909, F.4913 11 PLIP interactions: 10 interactions with chain K, 1 interactions with chain B Hydrophobic interactions: K:L.4840, K:Y.4841, K:F.4848, K:F.4848, K:F.4849, K:Y.4902, K:Y.4902, K:F.4906, K:T.4909, K:F.4913, B:F.4798

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

ATP.3: 14 residues within 4Å: Chain B: K.4201, K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.4945, B:F.4949, B:I.4950, B:H.4973, B:L.4975 Salt bridges: B:K.4201, B:K.4201, B:K.4204, B:K.4204, B:R.4205 ATP.8: 13 residues within 4Å: Chain E: K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:E.4945, E:F.4949, E:I.4950, E:H.4973, E:L.4975 Salt bridges: E:K.4201, E:K.4204, E:K.4204, E:R.4205 ATP.13: 13 residues within 4Å: Chain H: K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:E.4945, H:F.4949, H:I.4950, H:H.4973, H:L.4975 Salt bridges: H:K.4201, H:K.4204, H:K.4204, H:R.4205 ATP.18: 13 residues within 4Å: Chain K: K.4204, R.4205, M.4944, E.4945, K.4947, C.4948, F.4949, I.4950, F.4965, T.4969, H.4973, N.4974, L.4975 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:E.4945, K:F.4949, K:I.4950, K:H.4973, K:L.4975 Salt bridges: K:K.4201, K:K.4204, K:K.4204, K:R.4205

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 7 residues within 4Å: Chain B: F.3743, E.4229, I.4232, W.4706, I.4986, W.5001, 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.9: 6 residues within 4Å: Chain E: E.4229, I.4232, W.4706, I.4986, W.5001, Y.5004 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.5004 pi-Stacking: E:W.4706, E:W.4706, E:W.4706 CFF.14: 6 residues within 4Å: Chain H: E.4229, I.4232, W.4706, I.4986, W.5001, Y.5004 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Y.5004 pi-Stacking: H:W.4706, H:W.4706, H:W.4706 CFF.19: 6 residues within 4Å: Chain K: E.4229, I.4232, W.4706, I.4986, W.5001, Y.5004 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:Y.5004 pi-Stacking: K:W.4706, K:W.4706, K:W.4706

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain B: E.3883, E.3957, T.4991 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.3883, B:E.3957, B:T.4991 CA.10: 3 residues within 4Å: Chain E: E.3883, E.3957, T.4991 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.3883, E:E.3957, E:T.4991 CA.15: 3 residues within 4Å: Chain H: E.3883, E.3957, T.4991 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3883, H:E.3957, H:T.4991 CA.20: 3 residues within 4Å: Chain K: E.3883, E.3957, T.4991 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.3883, K:E.3957, K: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: ADGJ
Ryanodine receptor 1: BEHK
Nanobody 9657: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

D
L

G
J

J
F

B
I

E
A

H
D

K
G

C
K

F
C

I
E

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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