+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34379 | |||||||||
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Title | Cryo-EM structure of human CEPT1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CEPT1 / choline/ethanolamine phosphotransferase / LIPID BINDING PROTEIN | |||||||||
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 / phosphatidylcholine biosynthetic process / Synthesis of PC ...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 / phosphatidylcholine biosynthetic process / Synthesis of PC / lipid metabolic process / nuclear membrane / endoplasmic reticulum membrane / Golgi apparatus / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Qian HW / Wang ZH | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34379.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-34379-v30.xml emd-34379.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_34379.png | 61.6 KB | ||
Filedesc metadata | emd-34379.cif.gz | 5.4 KB | ||
Others | emd_34379_half_map_1.map.gz emd_34379_half_map_2.map.gz | 27.8 MB 27.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34379 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34379 | HTTPS FTP |
-Validation report
Summary document | emd_34379_validation.pdf.gz | 753.6 KB | Display | EMDB validaton report |
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Full document | emd_34379_full_validation.pdf.gz | 753.2 KB | Display | |
Data in XML | emd_34379_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_34379_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34379 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34379 | HTTPS FTP |
-Related structure data
Related structure data | 8gyxMC 8gywC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34379.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34379_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34379_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Choline/ethanolaminephosphotransferase 1 complexed with PC
Entire | Name: Choline/ethanolaminephosphotransferase 1 complexed with PC |
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Components |
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-Supramolecule #1: Choline/ethanolaminephosphotransferase 1 complexed with PC
Supramolecule | Name: Choline/ethanolaminephosphotransferase 1 complexed with PC type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Choline/ethanolaminephosphotransferase 1
Macromolecule | Name: Choline/ethanolaminephosphotransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ethanolaminephosphotransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.69509 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 2 / Number of copies: 2 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 851097 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |