SMTL ID : 8qbd.1

Helical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture +PIP2/+sterol (DOPC, DOPE, DOPS, cholesterol, PI(4,5)P2 35:20:20:15:10)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

14 x I3P: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE(Non-covalent)

I3P.1: 6 residues within 4Å: Chain A: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.66 Salt bridges: A:K.63, A:K.63, A:K.66, A:R.126, A:K.130, A:K.130, A:R.133 I3P.3: 6 residues within 4Å: Chain B: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.66 Salt bridges: B:K.63, B:K.63, B:K.66, B:R.126, B:K.130, B:K.130, B:R.133 I3P.5: 6 residues within 4Å: Chain C: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:K.66 Salt bridges: C:K.63, C:K.63, C:K.66, C:R.126, C:K.130, C:K.130, C:R.133 I3P.7: 6 residues within 4Å: Chain D: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.8 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.66 Salt bridges: D:K.63, D:K.63, D:K.66, D:R.126, D:K.130, D:K.130, D:R.133 I3P.9: 6 residues within 4Å: Chain E: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.10 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:K.66 Salt bridges: E:K.63, E:K.63, E:K.66, E:R.126, E:K.130, E:K.130, E:R.133 I3P.11: 6 residues within 4Å: Chain F: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.12 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:K.66 Salt bridges: F:K.63, F:K.63, F:K.66, F:R.126, F:K.130, F:K.130, F:R.133 I3P.13: 6 residues within 4Å: Chain G: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.14 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:K.66 Salt bridges: G:K.63, G:K.63, G:K.66, G:R.126, G:K.130, G:K.130, G:R.133 I3P.15: 6 residues within 4Å: Chain H: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.16 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:K.66 Salt bridges: H:K.63, H:K.63, H:K.66, H:R.126, H:K.130, H:K.130, H:R.133 I3P.17: 6 residues within 4Å: Chain I: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.18 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:K.66 Salt bridges: I:K.63, I:K.63, I:K.66, I:R.126, I:K.130, I:K.130, I:R.133 I3P.19: 6 residues within 4Å: Chain J: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.20 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:K.66 Salt bridges: J:K.63, J:K.63, J:K.66, J:R.126, J:K.130, J:K.130, J:R.133 I3P.21: 6 residues within 4Å: Chain K: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.22 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:K.66 Salt bridges: K:K.63, K:K.63, K:K.66, K:R.126, K:K.130, K:K.130, K:R.133 I3P.23: 6 residues within 4Å: Chain L: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.24 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:K.66 Salt bridges: L:K.63, L:K.63, L:K.66, L:R.126, L:K.130, L:K.130, L:R.133 I3P.25: 6 residues within 4Å: Chain M: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.26 8 PLIP interactions: 8 interactions with chain M Hydrogen bonds: M:K.66 Salt bridges: M:K.63, M:K.63, M:K.66, M:R.126, M:K.130, M:K.130, M:R.133 I3P.27: 6 residues within 4Å: Chain N: K.63, K.66, R.126, K.130, R.133 Ligands: P5S.28 8 PLIP interactions: 8 interactions with chain N Hydrogen bonds: N:K.66 Salt bridges: N:K.63, N:K.63, N:K.66, N:R.126, N:K.130, N:K.130, N:R.133

14 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.2: 9 residues within 4Å: Chain A: A.39, F.42, R.43, K.63, K.66, R.70 Chain B: G.30, F.32 Ligands: I3P.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.39 Hydrogen bonds: A:K.63, A:K.63 Salt bridges: A:R.43, A:K.66 P5S.4: 9 residues within 4Å: Chain A: G.30, F.32 Chain B: A.39, F.42, R.43, K.63, K.66, R.70 Ligands: I3P.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.39 Hydrogen bonds: B:K.63, B:K.63 Salt bridges: B:R.43, B:K.66 P5S.6: 9 residues within 4Å: Chain C: A.39, F.42, R.43, K.63, K.66, R.70 Chain D: G.30, F.32 Ligands: I3P.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.39 Hydrogen bonds: C:K.63, C:K.63 Salt bridges: C:R.43, C:K.66 P5S.8: 9 residues within 4Å: Chain C: G.30, F.32 Chain D: A.39, F.42, R.43, K.63, K.66, R.70 Ligands: I3P.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.39 Hydrogen bonds: D:K.63, D:K.63 Salt bridges: D:R.43, D:K.66 P5S.10: 9 residues within 4Å: Chain E: A.39, F.42, R.43, K.63, K.66, R.70 Chain F: G.30, F.32 Ligands: I3P.9 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:A.39 Hydrogen bonds: E:K.63, E:K.63 Salt bridges: E:R.43, E:K.66 P5S.12: 9 residues within 4Å: Chain E: G.30, F.32 Chain F: A.39, F.42, R.43, K.63, K.66, R.70 Ligands: I3P.11 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:A.39 Hydrogen bonds: F:K.63, F:K.63 Salt bridges: F:R.43, F:K.66 P5S.14: 9 residues within 4Å: Chain G: A.39, F.42, R.43, K.63, K.66, R.70 Chain H: G.30, F.32 Ligands: I3P.13 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:A.39 Hydrogen bonds: G:K.63, G:K.63 Salt bridges: G:R.43, G:K.66 P5S.16: 9 residues within 4Å: Chain G: G.30, F.32 Chain H: A.39, F.42, R.43, K.63, K.66, R.70 Ligands: I3P.15 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:A.39 Hydrogen bonds: H:K.63, H:K.63 Salt bridges: H:R.43, H:K.66 P5S.18: 9 residues within 4Å: Chain I: A.39, F.42, R.43, K.63, K.66, R.70 Chain J: G.30, F.32 Ligands: I3P.17 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:A.39 Hydrogen bonds: I:K.63, I:K.63 Salt bridges: I:R.43, I:K.66 P5S.20: 9 residues within 4Å: Chain I: G.30, F.32 Chain J: A.39, F.42, R.43, K.63, K.66, R.70 Ligands: I3P.19 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:A.39 Hydrogen bonds: J:K.63, J:K.63 Salt bridges: J:R.43, J:K.66 P5S.22: 9 residues within 4Å: Chain K: A.39, F.42, R.43, K.63, K.66, R.70 Chain L: G.30, F.32 Ligands: I3P.21 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:A.39 Hydrogen bonds: K:K.63, K:K.63 Salt bridges: K:R.43, K:K.66 P5S.24: 9 residues within 4Å: Chain K: G.30, F.32 Chain L: A.39, F.42, R.43, K.63, K.66, R.70 Ligands: I3P.23 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:A.39 Hydrogen bonds: L:K.63, L:K.63 Salt bridges: L:R.43, L:K.66 P5S.26: 9 residues within 4Å: Chain M: A.39, F.42, R.43, K.63, K.66, R.70 Chain N: G.30, F.32 Ligands: I3P.25 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:A.39 Hydrogen bonds: M:K.63, M:K.63 Salt bridges: M:R.43, M:K.66 P5S.28: 9 residues within 4Å: Chain M: G.30, F.32 Chain N: A.39, F.42, R.43, K.63, K.66, R.70 Ligands: I3P.27 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:A.39 Hydrogen bonds: N:K.63, N:K.63 Salt bridges: N:R.43, N:K.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kefauver, J.M. et al., Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain. Nature (2024)

Release Date

2024-07-24

Peptides

Sphingolipid long chain base-responsive protein PIL1: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
I

E
D

F
J

G
E

H
K

I
F

J
L

K
G

L
M

M
H

N
N

Sphingolipid long chain base-responsive protein PIL1

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