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- EMDB-64091: Cryo-EM structure of human choline-phosphotransferase 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-64091
TitleCryo-EM structure of human choline-phosphotransferase 1
Map data
Sample
  • Complex: Choline-phosphotransferase 1
    • Protein or peptide: Cholinephosphotransferase 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: MAGNESIUM ION
Keywordsphosphotransferase / MEMBRANE PROTEIN
Function / homology
Function and homology information


platelet activating factor biosynthetic process / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / CDP-choline pathway / diacylglycerol binding / phosphatidylcholine biosynthetic process / Synthesis of PC / intracellular membrane-bounded organelle / lipid metabolic process / regulation of cell growth ...platelet activating factor biosynthetic process / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / CDP-choline pathway / diacylglycerol binding / phosphatidylcholine biosynthetic process / Synthesis of PC / intracellular membrane-bounded organelle / lipid metabolic process / regulation of cell growth / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / membrane / metal ion binding
Similarity search - Function
Choline/ethanolamine phosphotransferase / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature.
Similarity search - Domain/homology
Cholinephosphotransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsHe YL / Qian HW
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Biochem Biophys Res Commun / Year: 2025
Title: Structural basis for substrate selectivity and evolutionary insights into human choline phosphotransferase 1.
Authors: Yonglin He / Yufan Yang / Meng Yang / Hongwu Qian /
Abstract: Phosphatidylcholine (PC) and phosphatidylethanolamine (PE), the core phospholipids maintaining eukaryotic membrane structure and function, are predominantly synthesized through the Kennedy pathway. ...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.
History
DepositionApr 9, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64091.png

Downloads & links

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Map

FileDownload / File: emd_64091.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.343
Minimum - Maximum-1.5708715 - 2.359216
Average (Standard dev.)0.0051273266 (±0.059885208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64091_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #2

Fileemd_64091_half_map_2.map
Projections & Slices
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Sample components

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Entire : Choline-phosphotransferase 1

EntireName: Choline-phosphotransferase 1
Components
  • Complex: Choline-phosphotransferase 1
    • Protein or peptide: Cholinephosphotransferase 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Choline-phosphotransferase 1

SupramoleculeName: Choline-phosphotransferase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.1 kDa/nm

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Macromolecule #1: Cholinephosphotransferase 1

MacromoleculeName: Cholinephosphotransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: diacylglycerol cholinephosphotransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.131707 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGAGAGSA PRWLRALSEP LSAAQLRRLE EHRYSAAGVS LLEPPLQLYW TWLLQWIPLW MAPNSITLLG LAVNVVTTLV LISYCPTAT EEAPYWTYLL CALGLFIYQS LDAIDGKQAR RTNSCSPLGE LFDHGCDSLS TVFMAVGASI AARLGTYPDW F FFCSFIGM ...String:
MAAGAGAGSA PRWLRALSEP LSAAQLRRLE EHRYSAAGVS LLEPPLQLYW TWLLQWIPLW MAPNSITLLG LAVNVVTTLV LISYCPTAT EEAPYWTYLL CALGLFIYQS LDAIDGKQAR RTNSCSPLGE LFDHGCDSLS TVFMAVGASI AARLGTYPDW F FFCSFIGM FVFYCAHWQT YVSGMLRFGK VDVTEIQIAL VIVFVLSAFG GATMWDYTIP ILEIKLKILP VLGFLGGVIF SC SNYFHVI LHGGVGKNGS TIAGTSVLSP GLHIGLIIIL AIMIYKKSAT DVFEKHPCLY ILMFGCVFAK VSQKLVVAHM TKS ELYLQD TVFLGPGLLF LDQYFNNFID EYVVLWMAMV ISSFDMVIYF SALCLQISRH LHLNIFKTAC HQAPEQVQVL SSKS HQNNM D

UniProtKB: Cholinephosphotransferase 1

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 295158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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