SMTL ID : 8qbb.1

Helical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture +PIP2/-sterol (DOPC, DOPE, DOPS, PI(4,5)P2 50:20:20:10)

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: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.43, A:R.43, A:K.66, A:R.133 Salt bridges: A:R.43, A:K.66, A:R.126, A:K.130, A:K.130 I3P.2: 6 residues within 4Å: Chain B: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.43, B:R.43, B:K.66, B:R.133 Salt bridges: B:R.43, B:K.66, B:R.126, B:K.130, B:K.130 I3P.3: 6 residues within 4Å: Chain C: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.43, C:R.43, C:K.66, C:R.133 Salt bridges: C:R.43, C:K.66, C:R.126, C:K.130, C:K.130 I3P.4: 6 residues within 4Å: Chain D: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.43, D:R.43, D:K.66, D:R.133 Salt bridges: D:R.43, D:K.66, D:R.126, D:K.130, D:K.130 I3P.5: 6 residues within 4Å: Chain E: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:R.43, E:R.43, E:K.66, E:R.133 Salt bridges: E:R.43, E:K.66, E:R.126, E:K.130, E:K.130 I3P.6: 6 residues within 4Å: Chain F: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:R.43, F:R.43, F:K.66, F:R.133 Salt bridges: F:R.43, F:K.66, F:R.126, F:K.130, F:K.130 I3P.7: 6 residues within 4Å: Chain G: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:R.43, G:R.43, G:K.66, G:R.133 Salt bridges: G:R.43, G:K.66, G:R.126, G:K.130, G:K.130 I3P.8: 6 residues within 4Å: Chain H: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:R.43, H:R.43, H:K.66, H:R.133 Salt bridges: H:R.43, H:K.66, H:R.126, H:K.130, H:K.130 I3P.9: 6 residues within 4Å: Chain I: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:R.43, I:R.43, I:K.66, I:R.133 Salt bridges: I:R.43, I:K.66, I:R.126, I:K.130, I:K.130 I3P.10: 6 residues within 4Å: Chain J: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:R.43, J:R.43, J:K.66, J:R.133 Salt bridges: J:R.43, J:K.66, J:R.126, J:K.130, J:K.130 I3P.11: 6 residues within 4Å: Chain K: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:R.43, K:R.43, K:K.66, K:R.133 Salt bridges: K:R.43, K:K.66, K:R.126, K:K.130, K:K.130 I3P.12: 6 residues within 4Å: Chain L: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:R.43, L:R.43, L:K.66, L:R.133 Salt bridges: L:R.43, L:K.66, L:R.126, L:K.130, L:K.130 I3P.13: 6 residues within 4Å: Chain M: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:R.43, M:R.43, M:K.66, M:R.133 Salt bridges: M:R.43, M:K.66, M:R.126, M:K.130, M:K.130 I3P.14: 6 residues within 4Å: Chain N: R.43, V.62, K.66, R.126, K.130, R.133 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:R.43, N:R.43, N:K.66, N:R.133 Salt bridges: N:R.43, N:K.66, N:R.126, N:K.130, N:K.130

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
J

C
F

D
B

E
C

F
I

G
D

H
E

I
K

J
L

K
G

L
M

M
H

N
N

Sphingolipid long chain base-responsive protein PIL1

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