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

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Basic information

Entry
Database: PDB / ID: 9xdb
TitleStructure of Plasmodium vivax Perforin-like protein2 pore in acr form
ComponentsMAC/Perforin domain containing protein
KeywordsTOXIN / Plasmodium / Perforin-like protein / PvPLP2
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhang, Y. / Zhong, L.J. / Song, Y. / Gilbert, R.J.C. / Ni, T. / Yu, X.L.
Funding support Hong Kong, 1items
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, R.J.C. / Ni, T. / Yu, X.
History
DepositionOct 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAC/Perforin domain containing protein
B: MAC/Perforin domain containing protein
C: MAC/Perforin domain containing protein


Theoretical massNumber of molelcules
Total (without water)379,9823
Polymers379,9823
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein MAC/Perforin domain containing protein


Mass: 126660.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_123515 / Production host: Homo sapiens (human) / References: UniProt: A5JZX6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plasmodium vivax Perforin-like Protein2 Pore / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES, pH 7.5, 150 mM NaCl
SpecimenConc.: 0.656 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 27526 / Details: Movies were recorded using serialEM.

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.6.2particle selection
2Topazv0.2.5particle selection
3SerialEM4.2.0image acquisition
5cryoSPARCv4.6.2CTF correction
8UCSF Chimera1.16model fitting
9UCSF ChimeraX1.7.1model fitting
10Coot0.9.8model fitting
11ISOLDE1.6.0model fitting
13PHENIX1.21_5207model refinement
14cryoSPARCv4.6.2initial Euler assignment
15cryoSPARCv4.6.2final Euler assignment
17cryoSPARCv4.6.23D reconstruction
Image processingDetails: Falcon 4i Selectris X energy filter
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3626157
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68218 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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