› 7yjo

Electron Microscopy
2.8Å resolution

Cryo-EM structure of the monomeric atSPT-ORM1 (LCB2a-deltaN5) complex

Released:
DOI: 10.2210/pdb7yjo/pdb
PDB entry 7yjo coloured by chain, front view.
PDB entry 7yjo coloured by chain, side view.
PDB entry 7yjo coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Mechanism of sphingolipid homeostasis revealed by structural analysis of Arabidopsis SPT-ORM1 complex.
Liu P, Xie T, Wu X, Han G, Gupta SD, Zhang Z, Yue J, Dong F, Gable K, Niranjanakumari S, Li W, Wang L, Liu W, Yao R, Cahoon EB, Dunn TM, Gong X
OpenAccess logo Sci Adv 9 eadg0728 (2023)
PMID: 36989369
Related structures: EMD-33876

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-199739 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Long chain base biosynthesis protein 1 Chain: A
Molecule details ›
Chain: A
Length: 420 amino acids
Theoretical weight: 46.28 KDa
Source organism: Arabidopsis thaliana
Expression system: Homo sapiens
UniProt:
  • Canonical: Q94IB8 (Residues: 63-482; Coverage: 87%)
Gene names: AP22, At4g36480, C7A10.880, EMB2779, FBR11, LCB1
Sequence domains: Aminotransferase class I and II
Long chain base biosynthesis protein 2a Chain: B
Molecule details ›
Chain: B
Length: 485 amino acids
Theoretical weight: 53.93 KDa
Source organism: Arabidopsis thaliana
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9LSZ9 (Residues: 6-489; Coverage: 99%)
Gene names: At5g23670, LCB2, LCB2a, MQM1.6
Sequence domains: Aminotransferase class I and II
ORMDL family protein Chain: D
Molecule details ›
Chain: D
Length: 157 amino acids
Theoretical weight: 18.22 KDa
Source organism: Arabidopsis thaliana
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9C5I0 (Residues: 1-157; Coverage: 100%)
Gene names: ATORM1, At1g01230, F6F3.4, F6F3_4
Sequence domains: ORMDL family
Long chain base biosynthesis protein 1 Chain: E
Molecule details ›
Chain: E
Length: 62 amino acids
Theoretical weight: 6.95 KDa
Source organism: Arabidopsis thaliana
Expression system: Homo sapiens
UniProt:
  • Canonical: Q94IB8 (Residues: 1-62; Coverage: 13%)
Gene names: AP22, At4g36480, C7A10.880, EMB2779, FBR11, LCB1
Transmembrane protein, putative (DUF3317) Chain: C
Molecule details ›
Chain: C
Length: 77 amino acids
Theoretical weight: 9.44 KDa
Source organism: Arabidopsis thaliana
Expression system: Homo sapiens
UniProt:
  • Canonical: A8MSB8 (Residues: 1-56; Coverage: 100%)
Gene names: At1g06515, SSSPTA
Sequence domains: Small subunit of serine palmitoyltransferase-like

Ligands and Environments

2 bound ligands:
Ligand PLS 1 x PLS
Ligand Z1T 1 x Z1T
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-33876
Expression system: Homo sapiens

Quick links

Citations

2 citation in other articles

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