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- EMDB-62715: Cryo-EM structure of human lipid phosphate phosphatase 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-62715
TitleCryo-EM structure of human lipid phosphate phosphatase 1
Map datamap
Sample
  • Complex: Phospholipid phosphatase 1
    • Protein or peptide: Phospholipid phosphatase 1
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
Keywordsphosphatase / MEMBRANE PROTEIN
Function / homology
Function and homology information


2-lysophosphatidate phosphatase / sphingosine-1-phosphate phosphatase activity / ceramide-1-phosphate phosphatase activity / diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / Sphingolipid catabolism / phosphatidate phosphatase activity / sphingosine metabolic process / ceramide metabolic process ...2-lysophosphatidate phosphatase / sphingosine-1-phosphate phosphatase activity / ceramide-1-phosphate phosphatase activity / diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / Sphingolipid catabolism / phosphatidate phosphatase activity / sphingosine metabolic process / ceramide metabolic process / phospholipid dephosphorylation / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / sphingolipid catabolic process / androgen receptor signaling pathway / regulation of lipid metabolic process / nuclear receptor-mediated steroid hormone signaling pathway / phospholipid metabolic process / caveola / phospholipase C-activating G protein-coupled receptor signaling pathway / apical plasma membrane / membrane raft / negative regulation of cell population proliferation / signal transduction / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Phosphatidate (PA) phosphatase-related / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
Phospholipid phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsYang M / Qian HW
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Cryo-EM structure of human lipid phosphate phosphatase 1
Authors: Yang M / Qian HW
History
DepositionDec 12, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62715.png

Downloads & links

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Map

FileDownload / File: emd_62715.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0647
Minimum - Maximum-0.40696168 - 0.6282287
Average (Standard dev.)0.0009397181 (±0.019488264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62715_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62715_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Phospholipid phosphatase 1

EntireName: Phospholipid phosphatase 1
Components
  • Complex: Phospholipid phosphatase 1
    • Protein or peptide: Phospholipid phosphatase 1
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate

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Supramolecule #1: Phospholipid phosphatase 1

SupramoleculeName: Phospholipid phosphatase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.2 kDa/nm

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Macromolecule #1: Phospholipid phosphatase 1

MacromoleculeName: Phospholipid phosphatase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.193031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFDKTRLPYV ALDVLCVLLA GLPFAILTSR HTPFQRGVFC NDESIKYPYK EDTIPYALLG GIIIPFSIIV IILGETLSVY CNLLHSNSF IRNNYIATIY KAIGTFLFGA AASQSLTDIA KYSIGRLRPH FLDVCDPDWS KINCSDGYIE YYICRGNAER V KEGRLSFY ...String:
MFDKTRLPYV ALDVLCVLLA GLPFAILTSR HTPFQRGVFC NDESIKYPYK EDTIPYALLG GIIIPFSIIV IILGETLSVY CNLLHSNSF IRNNYIATIY KAIGTFLFGA AASQSLTDIA KYSIGRLRPH FLDVCDPDWS KINCSDGYIE YYICRGNAER V KEGRLSFY SGHSSFSMYC MLFVALYLQA RMKGDWARLL RPTLQFGLVA VSIYVGLSRV SDYKHHWSDV LTGLIQGALV AI LVAVYVS DFFKERTSFK ERKEEDSHTT LHETPTTGNH YPSNHQP

UniProtKB: Phospholipid phosphatase 1

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Macromolecule #2: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 2 / Number of copies: 4 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 4 / Number of copies: 4 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tr...

MacromoleculeName: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
type: ligand / ID: 5 / Number of copies: 4 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142002
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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