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- PDB-8gyx: Cryo-EM structure of human CEPT1 -

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Basic information

Entry
Database: PDB / ID: 8gyx
TitleCryo-EM structure of human CEPT1
ComponentsCholine/ethanolaminephosphotransferase 1
KeywordsLIPID BINDING PROTEIN / CEPT1 / choline/ethanolamine phosphotransferase
Function / homology
Function and homology information


ethanolaminephosphotransferase / 1-alkenyl-2-acylglycerol choline phosphotransferase / 1-alkenyl-2-acylglycerol choline phosphotransferase activity / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / ethanolaminephosphotransferase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / Synthesis of PC / lipid metabolic process ...ethanolaminephosphotransferase / 1-alkenyl-2-acylglycerol choline phosphotransferase / 1-alkenyl-2-acylglycerol choline phosphotransferase activity / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / ethanolaminephosphotransferase 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
Chem-POV / Choline/ethanolaminephosphotransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQian, H.W. / Wang, Z.H.
Funding support China, 1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Choline/ethanolaminephosphotransferase 1
A: Choline/ethanolaminephosphotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0088
Polymers85,3902
Non-polymers1,6176
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Choline/ethanolaminephosphotransferase 1 / hCEPT1 / 1-alkenyl-2-acylglycerol choline phosphotransferase


Mass: 42695.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEPT1, PRO1101 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q9Y6K0, ethanolaminephosphotransferase, diacylglycerol cholinephosphotransferase, 1-alkenyl-2-acylglycerol choline phosphotransferase
#2: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Choline/ethanolaminephosphotransferase 1 complexed with PC
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 851097 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076286
ELECTRON MICROSCOPYf_angle_d1.3498544
ELECTRON MICROSCOPYf_dihedral_angle_d8.799882
ELECTRON MICROSCOPYf_chiral_restr0.075978
ELECTRON MICROSCOPYf_plane_restr0.0091040

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