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- PDB-21nw: Cryo-EM structure of human Lipid Phosphate Phosphatase 2 -

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Basic information

Entry
Database: PDB / ID: 21nw
TitleCryo-EM structure of human Lipid Phosphate Phosphatase 2
ComponentsPhospholipid phosphatase 2
KeywordsHYDROLASE / phosphatidylcholine
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
Chem-CPL / Phospholipid phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang, W.Y. / Han, L.
Funding support China, 3items
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, W.Y. / Han, L.
History
DepositionDec 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipid phosphatase 2
B: Phospholipid phosphatase 2
C: Phospholipid phosphatase 2
D: Phospholipid phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,35212
Polymers130,4354
Non-polymers3,9178
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Phospholipid phosphatase 2 / Lipid phosphate phosphohydrolase 2 / PAP2-gamma / PAP2-G / Phosphatidate phosphohydrolase type 2c / ...Lipid phosphate phosphohydrolase 2 / PAP2-gamma / PAP2-G / Phosphatidate phosphohydrolase type 2c / Phosphatidic acid phosphatase 2c / PAP-2c / PAP2c


Mass: 32608.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLPP2, LPP2, PPAP2C / Production host: Homo sapiens (human)
References: UniProt: O43688, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, phosphatidate phosphatase
#2: Chemical
ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of human Lipid Phosphate Phosphatase 2 and phosphatidylcholine(PC)
Type: COMPLEX / Details: C4 / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67525 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027796
ELECTRON MICROSCOPYf_angle_d0.39810608
ELECTRON MICROSCOPYf_dihedral_angle_d10.5241152
ELECTRON MICROSCOPYf_chiral_restr0.0361228
ELECTRON MICROSCOPYf_plane_restr0.0031288

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