9UET | pdb_00009uet

Cryo-EM structure of human choline-phosphotransferase 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural basis for substrate selectivity and evolutionary insights into human choline phosphotransferase 1.

He, Y.Yang, Y.Yang, M.Qian, H.

(2025) Biochem Biophys Res Commun 773: 152082-152082

  • DOI: https://doi.org/10.1016/j.bbrc.2025.152082
  • Primary Citation Related Structures: 
    9UET

  • PubMed Abstract: 

    Phosphatidylcholine (PC) and phosphatidylethanolamine (PE), the core phospholipids maintaining eukaryotic membrane structure and function, are predominantly synthesized through the Kennedy pathway. The final step of this pathway is catalyzed by choline phosphotransferase 1 (CHPT1) and choline ethanolamine phosphotransferase 1 (CEPT1). Notably, although these enzymes show high sequence homology, CHPT1 specifically synthesizes PC while CEPT1 catalyzes both PC and PE production, and the mechanism of this substrate selectivity remains unclear. Here, we report the 3.7 Å cryo-EM structure of human CHPT1 (hCHPT1), revealing a homodimer in which each monomer consists of an N-terminal domain, a catalytic domain, and a dimerization domain. Through structural and sequence analyses, along with biochemical characterizations, we identified important residues in the catalytic domain that regulate substrate selectivity. Moreover, cross-species sequence alignment showed ovipara CHPT1 conserves important substrate selectivity residues with CEPT1. This residues conservation may endow ovipara CHPT1 with catalytic bifunctionality comparable to CEPT1. These findings not only elucidate the structural basis for substrate selectivity between CHPT1 and CEPT1, but also provide novel evolutionary perspectives on phospholipid synthase adaptation.


  • Organizational Affiliation
    • Department of Cardiology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.

Macromolecule Content 

  • Total Structure Weight: 91.88 kDa 
  • Atom Count: 5,906 
  • Modeled Residue Count: 736 
  • Deposited Residue Count: 812 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholinephosphotransferase 1
A, B
406Homo sapiensMutation(s): 0 
Gene Names: CHPT1CPT1MSTP022
EC: 2.7.8.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUD6 (Homo sapiens)
Explore Q8WUD6 
Go to UniProtKB:  Q8WUD6
GTEx:  ENSG00000111666 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUD6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2026-07-01
    Changes: Data collection, Database references