[English] 日本語
Yorodumi
- EMDB-42500: Cholinephosphotransferase in complex with selective inhibitor che... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42500
TitleCholinephosphotransferase in complex with selective inhibitor chelerythrine
Map dataPrimary map
Sample
  • Complex: yCPT1
    • Complex: yCPT1
      • Protein or peptide: Cholinephosphotransferase 1
    • Complex: nanobody25
  • Ligand: MAGNESIUM ION
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium
  • Ligand: water
Keywordslipid metabolism / phospholipid synthesis / membrane protein enzyme / choline metabolism / MEMBRANE PROTEIN
Function / homology
Function and homology information


Synthesis of PC / Synthesis of PE / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / CDP-choline pathway / mitochondrial outer membrane / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / 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
Cholinephosphotransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRoberts JR / Maeda S / Ohi MD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for catalysis and selectivity of phospholipid synthesis by eukaryotic choline-phosphotransferase.
Authors: Jacquelyn R Roberts / Yasuhiro Horibata / Frank E Kwarcinski / Vinson Lam / Ashleigh M Raczkowski / Akane Hubbard / Betsy White / Hiroyuki Sugimoto / Gregory G Tall / Melanie D Ohi / Shoji Maeda /
Abstract: Phospholipids are the most abundant component in lipid membranes and are essential for the structural and functional integrity of the cell. In eukaryotic cells, phospholipids are primarily ...Phospholipids are the most abundant component in lipid membranes and are essential for the structural and functional integrity of the cell. In eukaryotic cells, phospholipids are primarily synthesized de novo through the Kennedy pathway that involves multiple enzymatic processes. The terminal reaction is mediated by a group of cytidine-5'-diphosphate (CDP)-choline /CDP-ethanolamine-phosphotransferases (CPT/EPT) that use 1,2-diacylglycerol (DAG) and CDP-choline or CDP-ethanolamine to produce phosphatidylcholine (PC) or phosphatidylethanolamine (PE) that are the main phospholipids in eukaryotic cells. Here we present the structure of the yeast CPT1 in multiple substrate-bound states. Structural and functional analysis of these binding-sites reveal the critical residues for the DAG acyl-chain preference and the choline/ethanolamine selectivity. Additionally, we present the structure in complex with a potent inhibitor characterized in this study. The ensemble of structures allows us to propose the reaction mechanism for phospholipid biosynthesis by the family of CDP-alcohol phosphotransferases (CDP-APs).
History
DepositionOct 26, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42500.png

Downloads & links

-
Map

FileDownload / File: emd_42500.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.434
Minimum - Maximum-2.2978075 - 3.4421315
Average (Standard dev.)-0.0003760571 (±0.06493872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_42500_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_42500_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : yCPT1

EntireName: yCPT1
Components
  • Complex: yCPT1
    • Complex: yCPT1
      • Protein or peptide: Cholinephosphotransferase 1
    • Complex: nanobody25
  • Ligand: MAGNESIUM ION
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium
  • Ligand: water

-
Supramolecule #1: yCPT1

SupramoleculeName: yCPT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Supramolecule #2: yCPT1

SupramoleculeName: yCPT1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Supramolecule #3: nanobody25

SupramoleculeName: nanobody25 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Lama glama (llama)

-
Macromolecule #1: Cholinephosphotransferase 1

MacromoleculeName: Cholinephosphotransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S228c
Molecular weightTheoretical: 44.753988 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (ACE)GFFIPQSSL GNLKLYKYQS DDRSFLSNHV LRPFWRKFAT IFPLWMAPNL VTLLGFCFII FNVLTTLYYD PYFDQE SPR WTYFSYAIGL FLYQTFDACD GMHARRTGQQ GPLGELFDHC IDSINTTLSM IPVCSMTGMG YTYMTIFSQF AILCSFY LS TWEEYHTHKL ...String:
(ACE)GFFIPQSSL GNLKLYKYQS DDRSFLSNHV LRPFWRKFAT IFPLWMAPNL VTLLGFCFII FNVLTTLYYD PYFDQE SPR WTYFSYAIGL FLYQTFDACD GMHARRTGQQ GPLGELFDHC IDSINTTLSM IPVCSMTGMG YTYMTIFSQF AILCSFY LS TWEEYHTHKL YLAEFCGPVE GIIVLCISFI AVGIYGPQTI WHTKVAQFSW QDFVFDVETV HLMYAFCTGA LIFNIVTA H TNVVRYYESQ STKSATPSKT AENISKAVNG LLPFFAYFSS IFTLVLIQPS FISLALILSI GFSVAFVVGR MIIAHLTMQ PFPMVNFPFL IPTIQLVLYA FMVYVLDYQK GSIVSALVWM GLGLTLAIHG MFINDIIYDI TTFLDIYALS IKHPKEI

UniProtKB: Cholinephosphotransferase 1

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 6 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

-
Macromolecule #4: 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium

MacromoleculeName: 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium
type: ligand / ID: 4 / Number of copies: 2 / Formula: CTI
Molecular weightTheoretical: 348.372 Da
Chemical component information

ChemComp-CTI:
1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium / inhibitor, alkaloid*YM

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2990 / Average exposure time: 4.4 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4613867
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 371370
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7898


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial model fitting was done using a model superposition function into a 3D volume in Chimera and then Phenix.real_space_refine was used for flexible fitting.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8urt:
Cholinephosphotransferase in complex with selective inhibitor chelerythrine

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more