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- EMDB-80306: Cryo-EM Structure of PLPP3 -

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Basic information

Entry
Database: EMDB / ID: EMD-80306
TitleCryo-EM Structure of PLPP3
Map data
Sample
  • Cell: PLPP3
    • Protein or peptide: Phospholipid phosphatase 3
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsPhosphatase / MEMBRANE PROTEIN
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
Phospholipid phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLong T / Wu Y
Funding support1 items
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, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80306.png

Downloads & links

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Map

FileDownload / File: emd_80306.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0815
Minimum - Maximum-0.3718492 - 0.6295749
Average (Standard dev.)0.0008539076 (±0.015761875)
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_80306_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_80306_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : PLPP3

EntireName: PLPP3
Components
  • Cell: PLPP3
    • Protein or peptide: Phospholipid phosphatase 3
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: PLPP3

SupramoleculeName: PLPP3 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Phospholipid phosphatase 3

MacromoleculeName: Phospholipid phosphatase 3 / 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: 36.024758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QNYKYDKAIV PESKNGGSPA LNNNPRRSGS KRVLLICLDL FCLFMAGLPF LIIETSTIKP YHRGFYCNDE SIKYPLKTGE TINDAVLCA VGIVIAILAI ITGEFYRIYY LKKSRSTIQN PYVAALYKQV GCFLFGCAIS QSFTDIAKVS IGRLRPHFLS V CNPDFSQI ...String:
QNYKYDKAIV PESKNGGSPA LNNNPRRSGS KRVLLICLDL FCLFMAGLPF LIIETSTIKP YHRGFYCNDE SIKYPLKTGE TINDAVLCA VGIVIAILAI ITGEFYRIYY LKKSRSTIQN PYVAALYKQV GCFLFGCAIS QSFTDIAKVS IGRLRPHFLS V CNPDFSQI NCSEGYIQNY RCRGDDSKVQ EARKSFFSGH ASFSMYTMLY LVLYLQARFT WRGARLLRPL LQFTLIMMAF YT GLSRVSD HKHHPSDVLA GFAQGALVAC CIVFFVSDLF KTKTTLSLPA PAIRKEILSP VDIIDRNNHH NMMDYKDDDD K

UniProtKB: Phospholipid phosphatase 3

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Macromolecule #2: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 2 / 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 #3: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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 #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 4 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI MORGAGNI
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: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 289649
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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