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Yorodumi- EMDB-28557: Structure of Xenopus cholinephosphotransferase1 in complex with C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28557 | ||||||||||||
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Title | Structure of Xenopus cholinephosphotransferase1 in complex with CDP-choline | ||||||||||||
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Sample |
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Keywords | CDP-APs / phospholipid synthesis / TRANSFERASE | ||||||||||||
Function / homology | Function and homology information diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / ethanolaminephosphotransferase activity / phosphatidylethanolamine biosynthetic process / Golgi membrane / endoplasmic reticulum membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Wang L / Zhou M | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28557.map.gz | 28.7 MB | EMDB map data format | |
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Header (meta data) | emd-28557-v30.xml emd-28557.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_28557.png | 35.9 KB | ||
Filedesc metadata | emd-28557.cif.gz | 5.7 KB | ||
Others | emd_28557_half_map_1.map.gz emd_28557_half_map_2.map.gz | 27.7 MB 27.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28557 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28557 | HTTPS FTP |
-Validation report
Summary document | emd_28557_validation.pdf.gz | 695.8 KB | Display | EMDB validaton report |
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Full document | emd_28557_full_validation.pdf.gz | 695.3 KB | Display | |
Data in XML | emd_28557_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_28557_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28557 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28557 | HTTPS FTP |
-Related structure data
Related structure data | 8erpMC 8eroC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28557.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: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28557_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28557_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : homodimer of choline phosphotransferase 1
Entire | Name: homodimer of choline phosphotransferase 1 |
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Components |
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-Supramolecule #1: homodimer of choline phosphotransferase 1
Supramolecule | Name: homodimer of choline phosphotransferase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Macromolecule #1: Cholinephosphotransferase 1
Macromolecule | Name: Cholinephosphotransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: diacylglycerol cholinephosphotransferase |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 44.54223 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 3 / Number of copies: 20 / Formula: LBN |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-LBN: |
-Macromolecule #4: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM
Macromolecule | Name: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM type: ligand / ID: 4 / Number of copies: 2 / Formula: CDC |
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Molecular weight | Theoretical: 488.324 Da |
Chemical component information | ChemComp-CDC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS 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: 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 |
-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: 381720 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |