› 8c82

Electron Microscopy
3.4Å resolution

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

Released:
DOI: 10.2210/pdb8c82/pdb
PDB entry 8c82 coloured by chain, front view.
PDB entry 8c82 coloured by chain, side view.
PDB entry 8c82 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of the ceramide-bound SPOTS complex.
Schäfer JH, Körner C, Esch BM, Limar S, Parey K, Walter S, Januliene D, Moeller A, Fröhlich F
Nat Commun 14 6196 (2023)
PMID: 37794019
Related structures: EMD-16469

Function and Biology Details

Reaction catalysed: 
Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-231785 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Protein ORM1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 222 amino acids
Theoretical weight: 25.22 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53224 (Residues: 1-222; Coverage: 100%)
Gene names: ORM1, YGR038W
Sequence domains: ORMDL family
Serine palmitoyltransferase 1 Chains: B, F
Molecule details ›
Chains: B, F
Length: 558 amino acids
Theoretical weight: 62.27 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25045 (Residues: 1-558; Coverage: 100%)
Gene names: END8, LCB1, TSC2, YMR296C
Sequence domains: Aminotransferase class I and II
Serine palmitoyltransferase 2 Chains: C, G
Molecule details ›
Chains: C, G
Length: 561 amino acids
Theoretical weight: 63.19 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40970 (Residues: 1-561; Coverage: 100%)
Gene names: D4246, LCB2, SCS1, TSC1, YD9609.16, YDR062W
Sequence domains: Aminotransferase class I and II
Serine palmitoyltransferase-regulating protein TSC3 Chains: D, H
Molecule details ›
Chains: D, H
Length: 80 amino acids
Theoretical weight: 9.59 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E790 (Residues: 1-80; Coverage: 100%)
Gene names: TSC3, YBR058C-A

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
2 bound ligands:
Ligand Z8A 2 x Z8A
Ligand Q7G 2 x Q7G
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-16469
Expression system: Saccharomyces cerevisiae

Quick links

Citations

1 review citation

Mechanisms of Nonvesicular Ceramide Transport.
Clausmeyer et al. (2023)

1 mention without citation

Structure of the ceramide-bound SPOTS complex.
Schäfer et al. (2023)