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Yorodumi- PDB-8ero: Structure of Xenopus cholinephosphotransferase1 in complex with CDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ero | ||||||||||||
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Title | Structure of Xenopus cholinephosphotransferase1 in complex with CDP | ||||||||||||
Components | Cholinephosphotransferase 1 | ||||||||||||
Keywords | TRANSFERASE / CDP-APs / phospholipid synthesis | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Wang, L. / Zhou, M. | ||||||||||||
Funding support | United States, 3items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ero.cif.gz | 156.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ero.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ero.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/8ero ftp://data.pdbj.org/pub/pdb/validation_reports/er/8ero | HTTPS FTP |
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-Related structure data
Related structure data | 28556MC 8erpC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44542.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: chpt1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q4KLV1, diacylglycerol cholinephosphotransferase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-LBN / #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: homodimer of choline phosphotransferase 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 20000 nm / Nominal defocus min: 8000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 465752 / Symmetry type: POINT | ||||||||||||||||||||||||
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