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- EMDB-62722: Cryo-EM structure of human lipid phosphate phosphatase 1 complexe... -

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Basic information

Entry
Database: EMDB / ID: EMD-62722
TitleCryo-EM structure of human lipid phosphate phosphatase 1 complexed with VO4
Map data
Sample
  • Complex: Phospholipid phosphatase 1
    • Protein or peptide: Phospholipid phosphatase 1
  • 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
  • Ligand: VANADATE ION
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: water
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: 2.47 Å
AuthorsYang M / Qian HW
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Chem Biol / Year: 2026
Title: Structural basis for the catalytic mechanism of human lipid phosphate phosphatases.
Authors: Meng Yang / Chunping Sun / Yonglin He / Hongwu Qian /
Abstract: Lipid phosphate phosphatases (LPPs) catalyze the dephosphorylation of a broad range of bioactive lipid phosphates, including lysophosphatidic acid and sphingosine-1-phosphate, playing essential roles ...Lipid phosphate phosphatases (LPPs) catalyze the dephosphorylation of a broad range of bioactive lipid phosphates, including lysophosphatidic acid and sphingosine-1-phosphate, playing essential roles in embryonic vasculogenesis, cell differentiation and inflammation. Here we present the cryo-electron microscopic structure of human LPP1 as a tetramer with C4 symmetry. We capture the phosphohistidine intermediate state by using vanadate as a phosphate analog, where vanadate is coordinated by positively charged residues from three conserved motifs (C1, C2 and C3). Structural investigations of LPP1 variants with mutations in two catalytic histidine residues confirm that the histidine in the C2 motif facilitates phosphate bond cleavage. Enzymatic assays validate our structural observations. Additionally, a phosphatidylinositol 4,5-bisphosphate (PIP) molecule was discovered in the LPP1 structure, underscoring a potential regulatory role for PIP in the catalytic activity of LPP1.
History
DepositionDec 12, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62722.png

Downloads & links

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Map

FileDownload / File: emd_62722.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-0.47683263 - 0.96260524
Average (Standard dev.)0.00014916829 (±0.0234044)
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_62722_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62722_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-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
  • Ligand: VANADATE ION
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: water

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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-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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 #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 3 / 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 #4: [(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: 4 / Number of copies: 4 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

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Macromolecule #5: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #6: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 6 / 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 #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 32 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 636414
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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