SMTL ID : 8duj.1

Global map in C1 of RyR1 particles in complex with ImperaCalcin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-4-4-4-mer

Ligands

4 x CFF: CAFFEINE(Non-covalent)

CFF.1: 8 residues within 4Å: Chain B: F.3753, E.4239, I.4242, F.4243, Q.4246, W.4716, I.4996, Y.5014 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:W.4716, B:W.4716 CFF.5: 9 residues within 4Å: Chain E: F.3753, E.4239, I.4242, F.4243, Q.4246, F.4671, W.4716, I.4996, Y.5014 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.4246 pi-Stacking: E:W.4716, E:W.4716 CFF.9: 7 residues within 4Å: Chain H: E.4239, I.4242, F.4243, F.4671, W.4716, I.4996, Y.5014 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:Y.5014 pi-Stacking: H:W.4716, H:W.4716 CFF.13: 6 residues within 4Å: Chain K: F.3753, E.4239, F.4243, W.4716, I.4996, Y.5014 2 PLIP interactions: 2 interactions with chain K pi-Stacking: K:W.4716, K:W.4716

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain B: E.3893, E.3967, T.5001 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.3893, B:E.3893, B:E.3967, B:E.3967, B:T.5001 CA.6: 6 residues within 4Å: Chain E: E.3893, H.3895, E.3967, Q.3970, T.5001, H.5003 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.5001 CA.10: 4 residues within 4Å: Chain H: E.3893, E.3967, T.5001, H.5003 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.3893, H:E.3893, H:E.3967, H:E.3967, H:T.5001 CA.14: 5 residues within 4Å: Chain K: E.3893, E.3967, Q.3970, T.5001, H.5003 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.3893, K:E.3967, K:E.3967, K:T.5001

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

ATP.3: 12 residues within 4Å: Chain B: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, T.4979, H.4983, N.4984, L.4985 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:F.4959, B:T.4979, B:H.4983, B:L.4985 Salt bridges: B:K.4211, B:K.4214, B:K.4214, B:R.4215 ATP.7: 12 residues within 4Å: Chain E: K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, T.4979, H.4983, N.4984, L.4985 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:E.4955, E:F.4959, E:I.4960, E:T.4979, E:H.4983, E:L.4985 Salt bridges: E:K.4214, E:R.4215, E:R.4215 ATP.11: 12 residues within 4Å: Chain H: K.4211, R.4215, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:F.4959, H:I.4960, H:T.4979, H:H.4983, H:L.4985 Salt bridges: H:K.4211, H:K.4211, H:R.4215 ATP.15: 12 residues within 4Å: Chain K: K.4211, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, T.4979, H.4983, N.4984, L.4985 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:C.4958, K:T.4979, K:L.4985 Salt bridges: K:K.4211, K:K.4211, K:R.4215, K:R.4215

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.8: 4 residues within 4Å: Chain E: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4958, E:C.4961, E:H.4978, E:H.4983 ZN.12: 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 ZN.16: 4 residues within 4Å: Chain K: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.4958, K:C.4961, K:H.4978, K:H.4983

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haji-Ghassemi, O. et al., Cryo-EM analysis of scorpion toxin binding to Ryanodine Receptors reveals subconductance that is abolished by PKA phosphorylation. Sci Adv (2023)

Release Date

2023-05-31

Peptides

Imperacalcin: A
Ryanodine receptor 1: BEHK
Peptidyl-prolyl cis-trans isomerase FKBP1B: CFIL
Calmodulin-1: DGJM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
G

E
A

H
D

K
J

C
H

F
B

I
E

L
K

D
I

G
C

J
F

M
L

Membrane

We predict this structure to be a membrane protein.
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Imperacalcin

Ryanodine receptor 1

Peptidyl-prolyl cis-trans isomerase FKBP1B

Calmodulin-1

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