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

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Open data


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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: Gupta J / Izard T
History
DepositionFeb 24, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 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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