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- EMDB-28557: Structure of Xenopus cholinephosphotransferase1 in complex with C... -

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Basic information

Entry
Database: EMDB / ID: EMD-28557
TitleStructure of Xenopus cholinephosphotransferase1 in complex with CDP-choline
Map data
Sample
  • Complex: homodimer of choline phosphotransferase 1
    • Protein or peptide: Cholinephosphotransferase 1
  • Ligand: MAGNESIUM ION
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM
KeywordsCDP-APs / phospholipid synthesis / TRANSFERASE
Function / homology
Function and homology information


diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / 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 speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang L / Zhou M
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122784 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086392 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R1223 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure of a eukaryotic cholinephosphotransferase-1 reveals mechanisms of substrate recognition and catalysis.
Authors: Lie Wang / Ming Zhou /
Abstract: Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic cell membranes. In eukaryotes, two highly homologous enzymes, cholinephosphotransferase-1 (CHPT1) and choline/ethanolamine ...Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic cell membranes. In eukaryotes, two highly homologous enzymes, cholinephosphotransferase-1 (CHPT1) and choline/ethanolamine phosphotransferase-1 (CEPT1) catalyze the final step of de novo PC synthesis. CHPT1/CEPT1 joins two substrates, cytidine diphosphate-choline (CDP-choline) and diacylglycerol (DAG), to produce PC, and Mg is required for the reaction. However, mechanisms of substrate recognition and catalysis remain unresolved. Here we report structures of a CHPT1 from Xenopus laevis (xlCHPT1) determined by cryo-electron microscopy to an overall resolution of ~3.2 Å. xlCHPT1 forms a homodimer, and each protomer has 10 transmembrane helices (TMs). The first 6 TMs carve out a cone-shaped enclosure in the membrane in which the catalysis occurs. The enclosure opens to the cytosolic side, where a CDP-choline and two Mg are coordinated. The structures identify a catalytic site unique to eukaryotic CHPT1/CEPT1 and suggest an entryway for DAG. The structures also reveal an internal pseudo two-fold symmetry between TM3-6 and TM7-10, and suggest that CHPT1/CEPT1 may have evolved from their distant prokaryotic ancestors through gene duplication.
History
DepositionOct 12, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28557.png

Downloads & links

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Map

FileDownload / File: emd_28557.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.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.97
Minimum - Maximum-4.687986 - 7.1804576
Average (Standard dev.)0.02270834 (±0.1787405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28557_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_28557_half_map_2.map
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Sample components

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Entire : homodimer of choline phosphotransferase 1

EntireName: homodimer of choline phosphotransferase 1
Components
  • Complex: homodimer of choline phosphotransferase 1
    • Protein or peptide: Cholinephosphotransferase 1
  • Ligand: MAGNESIUM ION
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM

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Supramolecule #1: homodimer of choline phosphotransferase 1

SupramoleculeName: homodimer of choline phosphotransferase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 44.54223 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGLAEGLAAR MAPHLYIQEP LSAQQLKKLE EHKYSASGRS LVEPPMQVYW NWLVEKVPLW LAPNTITMVG LLLNVLSTLI LVCYCPTAT EGAPFWTYLL CAIGLFVYQS LDAIDGKQAR RTNSSSPLGE MFDHGCDSIS IVFVNLGTIA AVRLGTLPGW M FYCCFVGM ...String:
MGLAEGLAAR MAPHLYIQEP LSAQQLKKLE EHKYSASGRS LVEPPMQVYW NWLVEKVPLW LAPNTITMVG LLLNVLSTLI LVCYCPTAT EGAPFWTYLL CAIGLFVYQS LDAIDGKQAR RTNSSSPLGE MFDHGCDSIS IVFVNLGTIA AVRLGTLPGW M FYCCFVGM FMFYCAQWQT YVCGTLKFGI IDVTELQISV TVMFLMTAVC GPELWDYEIP FTGLPMKTIP LLGIIGGTVY SC SNYFRVI LSGGVGKNGS TVAGTSVLSP GLHIGLVLLL ALMIYKKSTT NLFLQNPCLY TLAFGFVSAK ITIKLVIAHM TKS EISLQD TAFIGPGLLF FNQYFNSFID EYIVLWIAMV ISFADLLRYC ISVCLQIATH LRISVFRISS NQAAEQVQTQ KQKL TD

UniProtKB: Cholinephosphotransferase 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 3 / Number of copies: 20 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #4: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM

MacromoleculeName: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM
type: ligand / ID: 4 / Number of copies: 2 / Formula: CDC
Molecular weightTheoretical: 488.324 Da
Chemical component information

ChemComp-CDC:
[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 8.0 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 381720
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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