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- EMDB-66759: Plasmodium vivax Perforin-like protein 2 pore on membrane by cryo... -

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Basic information

Entry
Database: EMDB / ID: EMD-66759
TitlePlasmodium vivax Perforin-like protein 2 pore on membrane by cryoET subtomogram averaging
Map datalocal resolution map
Sample
  • Complex: Plasmodium vivax Perforin-like Protein2 Pore
KeywordsPlasmodium / Perforin-like protein / PvPLP2 / TOXIN
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Methodsubtomogram averaging / cryo EM / Resolution: 8.98 Å
AuthorsZhang Y / Zhong LJ / Song Y / Gilbert RJC / Ni T / Yu XL
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
Other governmentResearch Grant Council - General Research Fund Hong Kong
CitationJournal: Nat Commun / Year: 2026
Title: Molecular mechanism of pore formation by Plasmodium Perforin-like Protein 2
Authors: Zhang Y / Zhong L / Song Y / Guo M / Ren K / Yang T / Huang Y / Sirotkin I / Yi G / Jiao F / Zhang P / Gilbert RJC / Ni T / Yu X
History
DepositionOct 27, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66759.png

Downloads & links

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Map

FileDownload / File: emd_66759.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.14 Å/pix.
x 120 pix.
= 377.04 Å		3.14 Å/pix.
x 120 pix.
= 377.04 Å		3.14 Å/pix.
x 120 pix.
= 377.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.142 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.52476984 - 1.5445433
Average (Standard dev.)0.0000018337789 (±0.112440966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 377.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66759_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: postprocess map

Fileemd_66759_additional_1.map
Annotationpostprocess map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2 from reconstruction

Fileemd_66759_half_map_1.map
Annotationhalf map2 from reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1 from reconstruction

Fileemd_66759_half_map_2.map
Annotationhalf map1 from reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Plasmodium vivax Perforin-like Protein2 Pore

EntireName: Plasmodium vivax Perforin-like Protein2 Pore
Components
  • Complex: Plasmodium vivax Perforin-like Protein2 Pore

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Supramolecule #1: Plasmodium vivax Perforin-like Protein2 Pore

SupramoleculeName: Plasmodium vivax Perforin-like Protein2 Pore / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: EMS Lacey Carbon / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 4.0 e/Å2
Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme (group of 2) was used, with a tilt range of -45 ...Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme (group of 2) was used, with a tilt range of -45 to 45 at 3 degree increments (or -40 to 40 at 4 degree increments)and an exposure dose of 4 e-/A2 per image. The total dose was 124(or 84) e-/A2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v4) / Number subtomograms used: 91441
ExtractionNumber tomograms: 1235 / Number images used: 334526 / Software - Name: emClarity (ver. v1.6.2)
CTF correctionSoftware: (Name: emClarity (ver. v1.6.2), RELION (ver. v4)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. v4)
FSC plot (resolution estimation)

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