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- EMDB-49401: CryoEM Structure of PHR-phosphatase-C2 domain of SHIP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-49401
TitleCryoEM Structure of PHR-phosphatase-C2 domain of SHIP2
Map dataCoulomb potential map for SHIP2 PHR-PTase-C2
Sample
  • Organelle or cellular component: PHR-phosphatase-C2 domains of SHIP2
Keywordsinositol phosphatase / LIPID BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsGupta J / Izard T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci / Year: 2026
Title: Structural insights into SHIP2 reveal its membrane regulatory mechanisms.
Authors: Jyoti Gupta / Johanne Le Coq / Daniel Lietha / Tina Izard /
Abstract: Src homology 2 domain-containing inositol-5 phosphatase 2 (SHIP2) is a key player in regulating the signaling by phosphoinositides and is involved in the modulation of cellular functions such as ...Src homology 2 domain-containing inositol-5 phosphatase 2 (SHIP2) is a key player in regulating the signaling by phosphoinositides and is involved in the modulation of cellular functions such as proliferation, adhesion, migration, and survival. SHIP2 works by dephosphorylating PIP to modulate the PI3K/AKT pathway, which plays a role in different standard and pathological conditions. SHIP2 appears to play a dual part in cancer, serving as a tumor suppressor in some instances and a tumor promoter in others. It is also involved in neurodegenerative diseases, including Alzheimer's disease. To understand the molecular mechanism of SHIP2, we solved its cryogenic electron microscopy (cryoEM) structure. Unexpectedly, the SHIP2 pleckstrin homology-related domain was found to associate with its C2 and phosphatase domains. This arrangement enables the catalytic domain to interact with the substrate, especially at higher concentrations of PIP or PI(3,4)P. Furthermore, SHIP2 forms oligomers on the membrane. Our findings suggest a mechanism by which SHIP2 activity may be regulated through interactions with membrane lipids. This provides structural insights into how domain organization and membrane association regulate its function in various physiological contexts.
History
DepositionFeb 24, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49401.png

Downloads & links

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Map

FileDownload / File: emd_49401.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoulomb potential map for SHIP2 PHR-PTase-C2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 128 pix.
= 184.32 Å		1.44 Å/pix.
x 128 pix.
= 184.32 Å		1.44 Å/pix.
x 128 pix.
= 184.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0877
Minimum - Maximum-0.90927047 - 0.8941236
Average (Standard dev.)-0.00054871675 (±0.03691951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 184.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49401_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49401_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49401_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PHR-phosphatase-C2 domains of SHIP2

EntireName: PHR-phosphatase-C2 domains of SHIP2
Components
  • Organelle or cellular component: PHR-phosphatase-C2 domains of SHIP2

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Supramolecule #1: PHR-phosphatase-C2 domains of SHIP2

SupramoleculeName: PHR-phosphatase-C2 domains of SHIP2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68 KDa

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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

Concentration0.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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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: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 513600
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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