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- PDB-25qp: Cryo-EM Structure of PLPP3 -

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Basic information

Entry
Database: PDB / ID: 25qp
TitleCryo-EM Structure of PLPP3
ComponentsPhospholipid phosphatase 3
KeywordsMEMBRANE PROTEIN / Phosphatase
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 / positive regulation of endothelial cell-matrix adhesion / ceramide metabolic process / delta-catenin binding / phospholipid dephosphorylation ...sphingosine-1-phosphate phosphatase activity / ceramide-1-phosphate phosphatase activity / phosphatidate phosphatase / Sphingolipid catabolism / phosphatidate phosphatase activity / sphingosine metabolic process / positive regulation of endothelial cell-matrix adhesion / ceramide metabolic process / delta-catenin binding / phospholipid dephosphorylation / positive regulation of homotypic cell-cell adhesion / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cell-cell adhesion mediated by integrin / sphingolipid catabolic process / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phospholipid metabolic process / positive regulation of intracellular signal transduction / endoplasmic reticulum exit site / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell migration / integrin-mediated signaling pathway / adherens junction / trans-Golgi network / cell-cell adhesion / integrin binding / basolateral plasma membrane / protein stabilization / membrane raft / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / membrane / plasma membrane
Similarity search - Function
Phosphatidate (PA) phosphatase-related / Phosphatidic acid phosphatase type 2/haloperoxidase / Acid phosphatase homologues / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Phospholipid phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLong, T. / Wu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of PLPP3-mediated lipid phosphate dephosphorylation and its role in melanoma.
Authors: Yingjie Wu / Di Xiao / Xingfan Li / Keyu Wang / Hongxu Zhang / Yuanyuan Zhao / Di Wu / Ruxi Qi / Mi Zhou / Han Han / Tao Long /
Abstract: Lipid phosphates serve as signaling molecules involved in diverse cellular processes such as cell proliferation, migration, angiogenesis, inflammation, immunity and cancer progression. Phospholipid ...Lipid phosphates serve as signaling molecules involved in diverse cellular processes such as cell proliferation, migration, angiogenesis, inflammation, immunity and cancer progression. Phospholipid phosphatases (PLPPs) modulate these signals by catalyzing the dephosphorylation of lipid phosphates. Here, we report the cryo-EM structure of PLPP3, revealing a tetrameric assembly. PLPP3 contains six transmembrane helices (TMs) and an extracellular domain that contains two extracellular loops. TMs 1-4 create a hydrophobic cleft that holds the tails of a phospholipid while the extracellular domain forms a positively charged pocket to accommodate the polar head group. Two conserved catalytic histidine residues in this pocket coordinate a putative zinc ion previously identified as a PLPP3 inhibitor. Structural mapping of somatic mutations with functional analysis reveals that PLPP3 acts as a tumor suppressor in melanoma. Together, our findings provide critical insights into the structure, substrate engagement, inhibitory mechanism, and cancer-related function of PLPP3.
History
DepositionApr 14, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 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 3
B: Phospholipid phosphatase 3
C: Phospholipid phosphatase 3
D: Phospholipid phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,42820
Polymers144,0994
Non-polymers6,32916
Water724
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

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Phospholipid phosphatase 3 / Lipid phosphate phosphohydrolase 3 / PAP2-beta / Phosphatidate phosphohydrolase type 2b / ...Lipid phosphate phosphohydrolase 3 / PAP2-beta / Phosphatidate phosphohydrolase type 2b / Phosphatidic acid phosphatase 2b / PAP-2b / PAP2b / Vascular endothelial growth factor and type I collagen-inducible protein / VCIP


Mass: 36024.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLPP3, LPP3, PPAP2B / Production host: Homo sapiens (human)
References: UniProt: O14495, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, phosphatidate phosphatase
#5: 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
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

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Non-polymers , 4 types, 16 molecules

#2: Chemical
ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate


Mass: 760.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical
ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H52O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

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: PLPP3 / Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI MORGAGNI
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 289649 / Symmetry type: POINT

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