9XDB | pdb_00009xdb

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

• PDB DOI: https://doi.org/10.2210/pdb9XDB/pdb
• EM Map EMD-66761: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Plasmodium vivax
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-10-27 Released: 2026-08-12 
• Deposition Author(s): Zhang, Y., Zhong, L.J., Song, Y., Gilbert, R.J.C., Ni, T., Yu, X.L.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Molecular mechanism of pore formation by Plasmodium Perforin-like Protein 2.

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.

(2026) Nat Commun 17

• PubMed: 42675073 
• DOI: https://doi.org/10.1038/s41467-026-76236-6
• Primary Citation Related Structures: 
  9XDA, 9XDB


• PubMed Abstract: 
  

  Malaria-causing Plasmodium parasites must pass through several host cell types to complete their life cycle. This cell traversal is facilitated by perforin-like proteins (PLPs), among which PLP2 is essential for erythrocyte rupture by gametocytes. However, the mechanism by which PLP2 forms pores is not yet understood. Here, we combine cryo-electron microscopy and tomography to reveal the structural basis of Plasmodium vivax PLP2-mediated membrane attack. PvPLP2 assembles on lipid bilayers into heterogeneous arc- and ring-shaped pores with variable stoichiometries. Among them, we determine the structure of a 17-subunit pore complex in which the pore-forming MACPF domains form the central β-barrel, while the peripheral Apicomplexan PLP C-terminal β-pleated sheet (APCβ) domains anchor the complex to the membrane surface. A disulfide-stabilized mutant captures an intermediate pre-pore complex prior to membrane insertion, delineating the structural transitions that underpin β-barrel deployment. Functionally, PvPLP2 acts preferentially on the inner leaflet of the erythrocyte membrane, a specificity driven by its affinity for negatively charged lipids. Together, these findings establish the pore-formation pathway for a key Plasmodium virulence factor and provide a structural framework for rational design of transmission-blocking agents that prevent gametocyte egress.

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Organizational Affiliation: 
• School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China.
Department of Life Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China.
Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, PR China.
Materials Innovation Institute for Life Sciences and Energy (MILES), Shenzhen, China.
Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK. [e-mail].
School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China. [e-mail].
Materials Innovation Institute for Life Sciences and Energy (MILES), Shenzhen, China. [e-mail].
Department of Life Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 379.98 kDa 
• Atom Count: 13,698 
• Modeled Residue Count: 1,734 
• Deposited Residue Count: 3,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAC/Perforin domain containing protein	A, B, C	1,120	Plasmodium vivax	Mutation(s): 0  Gene Names: PVX_123515
UniProt
Find proteins for A5JZX6 (Plasmodium vivax (strain Salvador I)) Explore A5JZX6  Go to UniProtKB:  A5JZX6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC	v4.6.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Zhang, Y., Zhong, L.J., Song, Y., Gilbert, R.J.C., Ni, T., Yu, X.L.

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Funding Organization	Location	Grant Number
Other government	Hong Kong	Research Grant Council - General Research Fund

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release
  
• Version 1.1: 2026-09-16
  Changes: Data collection, Database references