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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 / regulation of cell growth / lipid metabolic process / Golgi membrane ...platelet activating factor biosynthetic process / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / CDP-choline pathway / diacylglycerol binding / phosphatidylcholine biosynthetic process / Synthesis of PC / regulation of cell growth / lipid metabolic process / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / metal ion binding / membrane
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: To Be Published
Title: Cryo-EM structure of human choline-phosphotransferase 1
Authors: He YL / Qian HW
History
DepositionApr 9, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64091_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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