› 8y2m

Electron Microscopy
3.07Å resolution

Cryo-EM structure of the FB1-bound Lac1-Lip1 complex

Released:
DOI: 10.2210/pdb8y2m/pdb
PDB entry 8y2m coloured by chain, front view.
PDB entry 8y2m coloured by chain, side view.
PDB entry 8y2m coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Mechanism of ceramide synthase inhibition by fumonisin B1.
Zhang Z, Fang Q, Xie T, Gong X
Structure 32 1419-1428.e4 (2024)
PMID: 38964337
Related structures: EMD-38857

Function and Biology Details

Reaction catalysed: 
A very-long-chain fatty acyl-CoA + a sphingoid base = a very-long-chain ceramide + CoA
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236506 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ceramide synthase LAC1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 428 amino acids
Theoretical weight: 50.29 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Homo sapiens
UniProt:
  • Canonical: P28496 (Residues: 1-418; Coverage: 100%)
Gene names: DGT1, LAC1, YKL008C, YKL156
Sequence domains: TLC domain
Ceramide synthase subunit LIP1 Chains: B, D
Molecule details ›
Chains: B, D
Length: 150 amino acids
Theoretical weight: 17.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Homo sapiens
UniProt:
  • Canonical: Q03579 (Residues: 1-150; Coverage: 100%)
Gene names: LIP1, YMR298W

Ligands and Environments

3 bound ligands:
Ligand 6PL 6 x 6PL
Ligand A1D5V 2 x A1D5V
Ligand 7PO 2 x 7PO
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.07Å
Relevant EMDB volumes: EMD-38857
Expression system: Homo sapiens

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