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- EMDB-66761: Structure of Plasmodium vivax Perforin-like protein2 pore in acr form -

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Basic information

Entry
Database: EMDB / ID: EMD-66761
TitleStructure of Plasmodium vivax Perforin-like protein2 pore in acr form
Map datalocal resolution map
Sample
  • Complex: Plasmodium vivax Perforin-like Protein2 Pore
    • Protein or peptide: MAC/Perforin domain containing protein
KeywordsPlasmodium / Perforin-like protein / PvPLP2 / TOXIN
Function / homologyMAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / MAC/Perforin domain containing protein
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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_66761.png

Downloads & links

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Map

FileDownload / File: emd_66761.map.gz / Format: CCP4 / Size: 178 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.)
0.96 Å/pix.
x 360 pix.
= 344.052 Å		0.96 Å/pix.
x 360 pix.
= 344.052 Å		0.96 Å/pix.
x 360 pix.
= 344.052 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9557 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.35103413 - 0.5226404
Average (Standard dev.)0.0009632758 (±0.012284839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 344.052 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66761_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EMReady map

Fileemd_66761_additional_1.map
AnnotationEMReady map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1 from refinement

Fileemd_66761_half_map_1.map
Annotationhalf map1 from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2 from refinement

Fileemd_66761_half_map_2.map
Annotationhalf map2 from refinement
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
    • Protein or peptide: MAC/Perforin domain containing protein

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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 / Macromolecule list: all
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax)

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Macromolecule #1: MAC/Perforin domain containing protein

MacromoleculeName: MAC/Perforin domain containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax)
Molecular weightTheoretical: 126.660586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GEISRYSLIH ENDDDYNLEK FNSSDFLNEE KSYIADVNSV EKSKRLQNGN GVFASNPLY GCFNRYALRS GRYGKDVANQ ERSAKSHEKK ETTKCAGNTC SSFMLIKAHR AGGHAVKKNE KNYNLCNLQR E ERSCEQIP ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GEISRYSLIH ENDDDYNLEK FNSSDFLNEE KSYIADVNSV EKSKRLQNGN GVFASNPLY GCFNRYALRS GRYGKDVANQ ERSAKSHEKK ETTKCAGNTC SSFMLIKAHR AGGHAVKKNE KNYNLCNLQR E ERSCEQIP SGKKKVGQAA TIKRHNYNSN MMDLTRKTDK QHLLHGLPED YPKEEKKNVH AEPSDLQSFS HFETDTVAPS NL KKNPKRE EKQIRIHGNS RRDEPPQNEL PHNEPPQNGA DDMVVPPSYN DSIGYSGGNY FEKEKFIQIK FPIKISSEAE EQD EEMNNE KEIMKELERQ ESLHTRSDAN FEKYTNKEGE RDNAQKGGKN FVNSKLGEDN IMGIFKNPYS LGSDNFFIKN EMED LKRIN SERKDEQYKD FDLRDALMGE TGSITNTQPL SGGTQMKENE NNALTNSPND GESHTAYDKG HNPDIDLSLK YLGLG YDII MGNPEGDPTI NIDPGFRGPV LQINIEEMRV NKDSNVNANG TTSPYGSGFR GGGLPYREST LLGDYTLEEH KPKLTP WVI PEHSCSQSKN VEEIQNLEQY KMELLSDVKV STPSIFPYSF SASAEYKNAI KKLKVQNNVI FMMKIYCLRY YTGIPTT TS WRFTDNFRNA MKKLPPNFDG LKEDSQCSYE YYMNKIHTPQ CEENVNKWMM FFKLHGTHVA HEIYLGGKII IKMNMEKD E YNKLKDNNIS IKTFFNLYFH KMGLSAAYSK QTQKLVSKFR TSKDVSILGG NPGLNIENST FFEKWVNSIN KNSMPIRTK LLPFSFFMDD PNMIQAYKDA LTFYGLTYGV QIFDHEKYSH VVLSIGEYLE KCTQKLYAGP PPGLLTCPLG SSLLMGFSLN LDFYKNKDL SNTNGIASCE QMKESCSGNG FGKKYSDIRI WALCSEKPLD FITQVVQQGE SPKITASCPG NLVILFGFAL M KGKGSSSA NKVDIYPCRT GQTSCSAVLQ NSKIKQSMIY IACVDKSTNG LENIQTFSKV KNMGHVNSDQ HEDDTSLSFA CP KNSSLVF GFSLEFHTNF SKARNNFTDC SKASNTCEIR GTQINTKLAF FKPDKYSLAI VAVCRARSEV PLRAGTKHHH HHH

UniProtKB: MAC/Perforin domain containing protein

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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

Concentration0.656 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES, pH 7.5, 150 mM NaCl
GridModel: EMS Lacey Carbon / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 27526 / Average electron dose: 40.0 e/Å2 / Details: Movies were recorded using serialEM.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFalcon 4i Selectris X energy filter
Particle selectionNumber selected: 3626157
CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 68218
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9xdb:
Structure of Plasmodium vivax Perforin-like protein2 pore in acr form

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