SMTL ID : 8c81.1

Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

3 x ERG: ERGOSTEROL(Non-covalent)

ERG.1: 3 residues within 4Å: Chain A: I.55, F.195, L.208 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.55, A:F.195, A:L.208 ERG.4: 5 residues within 4Å: Chain A: F.195, V.199 Chain B: T.43, Y.46 Ligands: ERG.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.43, A:F.195, A:V.199 ERG.5: 6 residues within 4Å: Chain A: T.194, L.202 Chain B: Y.46, Y.50, Y.88 Ligands: ERG.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.46, B:Y.88, B:Y.88

1 x Z8A: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide(Non-covalent)

Z8A.2: 19 residues within 4Å: Chain A: N.76, W.79, I.88, H.89, L.114, M.117, Y.119, G.122, M.126, I.130, P.134 Chain C: L.69, I.72, I.73, H.76, Y.110, Y.485, L.490 Ligands: Q7G.3 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.88, A:L.114, A:Y.119, A:I.130, A:P.134, C:L.69, C:I.72, C:I.73 Hydrogen bonds: C:Y.110

1 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.3: 10 residues within 4Å: Chain A: I.130, K.131, Q.220 Chain B: K.249 Chain C: H.76, M.83, K.87, N.105, F.106 Ligands: Z8A.2 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:K.131, A:Q.220, B:K.249, C:K.87, C:K.87

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.6: 10 residues within 4Å: Chain B: S.407, A.408 Chain C: M.224, G.225, Y.226, H.250, D.331, H.334, T.365, K.366 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:K.366 Hydrogen bonds: C:G.225, C:Y.226, B:S.407, B:A.408 Salt bridges: C:K.366 pi-Stacking: C:H.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schafer, J.H. et al., Structure of the ceramide-bound SPOTS complex. Nat Commun (2023)

Release Date

2023-10-11

Peptides

Protein ORM1: A
Serine palmitoyltransferase 1: B
Serine palmitoyltransferase 2: C
Serine palmitoyltransferase-regulating protein TSC3: D
Phosphatidylinositol-3-phosphatase SAC1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Protein ORM1

Serine palmitoyltransferase 1

Serine palmitoyltransferase 2

Serine palmitoyltransferase-regulating protein TSC3

Phosphatidylinositol-3-phosphatase SAC1

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