SMTL ID : 7m6a.1

High resolution structure of the membrane embedded skeletal muscle ryanodine receptor

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.1: 14 residues within 4Å: Chain B: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.4955, B:F.4959, B:I.4960, B:L.4985 Salt bridges: B:K.4211, B:K.4211, B:K.4214, B:K.4214, B:K.4214 ATP.5: 14 residues within 4Å: Chain F: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:E.4955, F:F.4959, F:I.4960, F:L.4985 Salt bridges: F:K.4211, F:K.4211, F:K.4214, F:K.4214, F:K.4214 ATP.9: 14 residues within 4Å: Chain G: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:E.4955, G:F.4959, G:I.4960, G:L.4985 Salt bridges: G:K.4211, G:K.4211, G:K.4214, G:K.4214, G:K.4214 ATP.13: 14 residues within 4Å: Chain H: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:E.4955, H:F.4959, H:I.4960, H:L.4985 Salt bridges: H:K.4211, H:K.4211, H:K.4214, H:K.4214, H:K.4214

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain B: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.3967, B:E.3967, B:T.5001 CA.6: 4 residues within 4Å: Chain F: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3967, F:E.3967, F:T.5001 CA.10: 4 residues within 4Å: Chain G: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3967, G:E.3967, G:T.5001 CA.14: 4 residues within 4Å: Chain H: E.3893, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3967, H:E.3967, H:T.5001

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4958, B:C.4961, B:H.4978, B:H.4983 ZN.7: 4 residues within 4Å: Chain F: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4958, F:C.4961, F:H.4978, F:H.4983 ZN.11: 4 residues within 4Å: Chain G: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4958, G:C.4961, G:H.4978, G:H.4983 ZN.15: 4 residues within 4Å: Chain H: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4958, H:C.4961, H:H.4978, H:H.4983

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 6 residues within 4Å: Chain B: F.3753, E.4239, W.4716, I.4996, W.5011, Q.5015 3 PLIP interactions: 3 interactions with chain B pi-Stacking: B:W.4716, B:W.4716, B:W.4716 CFF.8: 6 residues within 4Å: Chain F: F.3753, E.4239, W.4716, I.4996, W.5011, Q.5015 3 PLIP interactions: 3 interactions with chain F pi-Stacking: F:W.4716, F:W.4716, F:W.4716 CFF.12: 6 residues within 4Å: Chain G: F.3753, E.4239, W.4716, I.4996, W.5011, Q.5015 3 PLIP interactions: 3 interactions with chain G pi-Stacking: G:W.4716, G:W.4716, G:W.4716 CFF.16: 6 residues within 4Å: Chain H: F.3753, E.4239, W.4716, I.4996, W.5011, Q.5015 3 PLIP interactions: 3 interactions with chain H pi-Stacking: H:W.4716, H:W.4716, H:W.4716

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melville, Z. et al., High-resolution structure of the membrane-embedded skeletal muscle ryanodine receptor. Structure (2022)

Release Date

2021-09-08

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1B: ACDE
Ryanodine receptor 1: BFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

C
H

D
J

E
O

B
A

F
G

G
B

H
I

Membrane

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

Ryanodine receptor 1

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