SMTL ID : 7yiu.1

Cryo-EM structure of the C6-ceramide-bound SPT-ORMDL3 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: G.238, F.239, N.242, H.263, S.265, D.344, A.346, T.376, T.378, K.379 Chain E: F.287, S.288, A.289 8 PLIP interactions: 1 interactions with chain E, 7 interactions with chain A Hydrogen bonds: E:A.289, A:G.238, A:F.239, A:S.265, A:D.344 Hydrophobic interactions: A:H.263 Salt bridges: A:K.379 pi-Stacking: A:H.263

1 x 6CM: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE(Non-covalent)

6CM.2: 9 residues within 4Å: Chain A: G.79, L.83, Y.122, I.503 Chain C: N.13, F.63, P.71, H.85 Ligands: R16.3 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.13, C:H.85 Hydrophobic interactions: A:L.83, A:I.503

2 x R16: HEXADECANE(Non-covalent)

R16.3: 6 residues within 4Å: Chain A: Y.75, V.76 Chain C: S.25, L.28, A.29 Ligands: 6CM.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.76, C:L.28, C:A.29 R16.4: 3 residues within 4Å: Chain C: Y.26, H.56, M.60 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.26, C:M.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis. Nat Commun (2023)

Release Date

2023-07-05

Peptides

Serine palmitoyltransferase 2: A
Serine palmitoyltransferase 1: B
ORM1-like protein 3: C
Serine palmitoyltransferase small subunit A: D
Serine palmitoyltransferase 1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
D

D
C

E
A

Membrane

We predict this structure to be a membrane protein.
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Serine palmitoyltransferase 2

Serine palmitoyltransferase 1

ORM1-like protein 3

Serine palmitoyltransferase small subunit A

Serine palmitoyltransferase 1

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