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- EMDB-34379: Cryo-EM structure of human CEPT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-34379
TitleCryo-EM structure of human CEPT1
Map data
Sample
  • Complex: Choline/ethanolaminephosphotransferase 1 complexed with PC
    • Protein or peptide: Choline/ethanolaminephosphotransferase 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: MAGNESIUM ION
KeywordsCEPT1 / choline/ethanolamine phosphotransferase / LIPID BINDING PROTEIN
Function / homology
Function and homology information


ethanolaminephosphotransferase / 1-alkenyl-2-acylglycerol choline phosphotransferase / ethanolaminephosphotransferase activity / 1-alkenyl-2-acylglycerol choline phosphotransferase activity / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / Synthesis of PC / lipid metabolic process ...ethanolaminephosphotransferase / 1-alkenyl-2-acylglycerol choline phosphotransferase / ethanolaminephosphotransferase activity / 1-alkenyl-2-acylglycerol choline phosphotransferase activity / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / Synthesis of PC / lipid metabolic process / nuclear 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
Choline/ethanolaminephosphotransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQian HW / Wang ZH
Funding support China, 1 items
OrganizationGrant numberCountry
Other privateKY9100000034 China
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for catalysis of human choline/ethanolamine phosphotransferase 1.
Authors: Zhenhua Wang / Meng Yang / Yufan Yang / Yonglin He / Hongwu Qian /
Abstract: Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) are two primary components of the eukaryotic membrane and play essential roles in the maintenance of membrane integrity, lipid droplet ...Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) are two primary components of the eukaryotic membrane and play essential roles in the maintenance of membrane integrity, lipid droplet biogenesis, autophagosome formation, and lipoprotein formation and secretion. Choline/ethanolamine phosphotransferase 1 (CEPT1) catalyzes the last step of the biosynthesis of PC and PE in the Kennedy pathway by transferring the substituted phosphate group from CDP-choline/ethanolamine to diacylglycerol. Here, we present the cryo-EM structures of human CEPT1 and its complex with CDP-choline at resolutions of 3.7 Å and 3.8 Å, respectively. CEPT1 is a dimer with 10 transmembrane segments (TMs) in each protomer. TMs 1-6 constitute a conserved catalytic domain with an interior hydrophobic chamber accommodating a PC-like density. Structural observations and biochemical characterizations suggest that the hydrophobic chamber coordinates the acyl tails during the catalytic process. The PC-like density disappears in the structure of the complex with CDP-choline, suggesting a potential substrate-triggered product release mechanism.
History
DepositionSep 24, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34379.png

Downloads & links

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Map

FileDownload / File: emd_34379.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.5967696 - 3.7480774
Average (Standard dev.)0.004316493 (±0.10792702)
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: #2

Fileemd_34379_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34379_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/ethanolaminephosphotransferase 1 complexed with PC

EntireName: Choline/ethanolaminephosphotransferase 1 complexed with PC
Components
  • Complex: Choline/ethanolaminephosphotransferase 1 complexed with PC
    • Protein or peptide: Choline/ethanolaminephosphotransferase 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/ethanolaminephosphotransferase 1 complexed with PC

SupramoleculeName: Choline/ethanolaminephosphotransferase 1 complexed with PC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Choline/ethanolaminephosphotransferase 1

MacromoleculeName: Choline/ethanolaminephosphotransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ethanolaminephosphotransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.69509 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGCVLNKLFQ LPTPPLSRHQ LKRLEEHRYQ SAGRSLLEPL MQGYWEWLVR RVPSWIAPNL ITIIGLSINI CTTILLVFYC PTATEQAPL WAYIACACGL FIYQSLDAID GKQARRTNSS SPLGELFDHG CDSLSTVFVV LGTCIAVQLG TNPDWMFFCC F AGTFMFYC ...String:
TGCVLNKLFQ LPTPPLSRHQ LKRLEEHRYQ SAGRSLLEPL MQGYWEWLVR RVPSWIAPNL ITIIGLSINI CTTILLVFYC PTATEQAPL WAYIACACGL FIYQSLDAID GKQARRTNSS SPLGELFDHG CDSLSTVFVV LGTCIAVQLG TNPDWMFFCC F AGTFMFYC AHWQTYVSGT LRFGIIDVTE VQIFIIIMHL LAVIGGPPFW QSMIPVLNIQ MKIFPALCTV AGTIFSCTNY FR VIFTGGV GKNGSTIAGT SVLSPFLHIG SVITLAAMIY KKSAVQLFEK HPCLYILTFG FVSAKITNKL VVAHMTKSEM HLH DTAFIG PALLFLDQYF NSFIDEYIVL WIALVFSFFD LIRYCVSVCN QIASHLHIHV FRIK

UniProtKB: Choline/ethanolaminephosphotransferase 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 / POPC

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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

Concentration15 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 851097

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