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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 / endoplasmic reticulum / signal transduction / 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: To Be Published
Title: Cryo-EM structure of human Lipid Phosphate Phosphatase 2
Authors: Wang WY / Han L
History
DepositionDec 21, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 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

Projections

Slices (1/3)

Slices (1/2)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67854_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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