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- EMDB-67854: Cryo-EM structure of human Lipid Phosphate Phosphatase 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-67854
TitleCryo-EM structure of human Lipid Phosphate Phosphatase 2
Map data
Sample
  • Complex: Complex of human Lipid Phosphate Phosphatase 2 and phosphatidylcholine(PC)
    • Protein or peptide: Phospholipid phosphatase 2
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsphosphatidylcholine / HYDROLASE
Function / homology
Function and homology information


sphingosine-1-phosphate phosphatase activity / ceramide-1-phosphate phosphatase activity / phosphatidate phosphatase / Sphingolipid catabolism / phosphatidate phosphatase activity / sphingosine metabolic process / ceramide metabolic process / phospholipid dephosphorylation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / sphingolipid catabolic process ...sphingosine-1-phosphate phosphatase activity / ceramide-1-phosphate phosphatase activity / phosphatidate phosphatase / Sphingolipid catabolism / phosphatidate phosphatase activity / sphingosine metabolic process / ceramide metabolic process / phospholipid dephosphorylation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / sphingolipid catabolic process / phospholipid metabolic process / caveola / early endosome membrane / early endosome / endoplasmic reticulum membrane / signal transduction / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Phosphatidate (PA) phosphatase-related / Acid phosphatase homologues / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
Phospholipid phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang WY / Han L
Funding support China, 3 items
OrganizationGrant numberCountry
National Key R&D Program of China2024YFA1306103 China
National Natural Science Foundation of China (NSFC)32370766, 82573060 China
Fundamental Research Funds for the Central Universities2042025kf0001 China
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of human lipid phosphate phosphatase 2.
Authors: Wanyi Wang / Yue Xu / Peilin Guo / Han Han / Lei Han /
Abstract: Lipid phosphate phosphatases (LPPs) dephosphorylate lipid phosphates to regulate signaling and metabolism. Among the three mammalian isoforms, LPP1, LPP2, and LPP3, LPP2 has been strongly associated ...Lipid phosphate phosphatases (LPPs) dephosphorylate lipid phosphates to regulate signaling and metabolism. Among the three mammalian isoforms, LPP1, LPP2, and LPP3, LPP2 has been strongly associated with cancer, making it a potential therapeutic target. However, the molecular mechanisms underlying its structural organization, substrate recognition, and catalysis remain elusive. Here, we report the cryo-EM structure of human LPP2 (hLPP2). hLPP2 assembles as a homo-tetramer, with phosphatidylcholine bound in the substrate pocket. The tetrameric arrangement provides a structural basis for LPP oligomerization. The wide, open-ended substrate pocket explains the enzyme's broad substrate specificity. Structural comparison with PAP2 family members, including hG6PC1 and ecPgpB, suggests a conserved catalytic mechanism and highlights the regulatory role of residue E159 in stabilizing the catalytic center and phosphate release. Collectively, these findings advance our understanding of the structural basis and enzymatic mechanism of LPPs and may provide insights for the development of novel cancer therapies.
History
DepositionDec 21, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67854.png

Downloads & links

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Map

FileDownload / File: emd_67854.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.193
Minimum - Maximum-1.0122712 - 1.3717611
Average (Standard dev.)0.0012986504 (±0.033202283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67854_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: #1

Fileemd_67854_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human Lipid Phosphate Phosphatase 2 and phosphatidylch...

EntireName: Complex of human Lipid Phosphate Phosphatase 2 and phosphatidylcholine(PC)
Components
  • Complex: Complex of human Lipid Phosphate Phosphatase 2 and phosphatidylcholine(PC)
    • Protein or peptide: Phospholipid phosphatase 2
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of human Lipid Phosphate Phosphatase 2 and phosphatidylch...

SupramoleculeName: Complex of human Lipid Phosphate Phosphatase 2 and phosphatidylcholine(PC)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: C4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Phospholipid phosphatase 2

MacromoleculeName: Phospholipid phosphatase 2 / 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: 32.608721 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQRRWVFVLL DVLCLLVASL PFAILTLVNA PYKRGFYCGD DSIRYPYRPD TITHGLMAGV TITATVILVS AGEAYLVYTD RLYSRSDFN NYVAAVYKVL GTFLFGAAVS QSLTDLAKYM IGRLRPNFLA VCDPDWSRVN CSVYVQLEKV CRGNPADVTE A RLSFYSGH ...String:
MQRRWVFVLL DVLCLLVASL PFAILTLVNA PYKRGFYCGD DSIRYPYRPD TITHGLMAGV TITATVILVS AGEAYLVYTD RLYSRSDFN NYVAAVYKVL GTFLFGAAVS QSLTDLAKYM IGRLRPNFLA VCDPDWSRVN CSVYVQLEKV CRGNPADVTE A RLSFYSGH SSFGMYCMVF LALYVQARLC WKWARLLRPT VQFFLVAFAL YVGYTRVSDY KHHWSDVLVG LLQGALVAAL TV CYISDFF KARPPQHCLK EEELERKPSL SLTLTLGEAD HNHYGYPHSS S

UniProtKB: Phospholipid phosphatase 2

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Macromolecule #2: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 67525
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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