7CQI

Cryo-EM structure of the substrate-bound SPT-ORMDL3 complex

Summary for 7CQI

• Entry DOI: 10.2210/pdb7cqi/pdb
• EMDB information: 30080 30441
• Descriptor: Serine palmitoyltransferase 1, Serine palmitoyltransferase 2, ORM1-like protein 3, ... (6 entities in total)
• Functional Keywords: membrane protein, lipid synthesis, transferase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 5
• Total formula weight: 198228.91

Authors

Li, S.S.,Xie, T.,Wang, L.,Gong, X. (deposition date: 2020-08-11, release date: 2021-02-10, Last modification date: 2024-03-27)

Primary citation

Li, S.,Xie, T.,Liu, P.,Wang, L.,Gong, X.
Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
Nat.Struct.Mol.Biol., 28:249-257, 2021

PubMed Abstract: Human serine palmitoyltransferase (SPT) complex catalyzes the initial and rate-limiting step in the de novo biosynthesis of all sphingolipids. ORMDLs regulate SPT function, with human ORMDL3 being related to asthma. Here we report three high-resolution cryo-EM structures: the human SPT complex, composed of SPTLC1, SPTLC2 and SPTssa; the SPT-ORMDL3 complex; and the SPT-ORMDL3 complex bound to two substrates, PLP-L-serine (PLS) and a non-reactive palmitoyl-CoA analogue. SPTLC1 and SPTLC2 form a dimer of heterodimers as the catalytic core. SPTssa participates in acyl-CoA coordination, thereby stimulating the SPT activity and regulating the substrate selectivity. ORMDL3 is located in the center of the complex, serving to stabilize the SPT assembly. Our structural and biochemical analyses provide a molecular basis for the assembly and substrate selectivity of the SPT and SPT-ORMDL3 complexes, and lay a foundation for mechanistic understanding of sphingolipid homeostasis and for related therapeutic drug development.

PubMed: 33558762
DOI: 10.1038/s41594-020-00553-7

Experimental method

ELECTRON MICROSCOPY (3.2 Å)