9N10 | pdb_00009n10

P. falciparum P-type ATPase, PfATP4

• PDB DOI: https://doi.org/10.2210/pdb9N10/pdb
• EM Map EMD-48801: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Plasmodium falciparum Dd2
• Mutation(s): No 


• Deposited: 2025-01-24 Released: 2025-10-15 
• Deposition Author(s): Haile, M.T., Zhen, J., Ho, C.
• Funding Organization(s): National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Endogenous structure of antimalarial target PfATP4 reveals an apicomplexan-specific P-type ATPase modulator.

Haile, M.T., Shukla, A., Zhen, J., Mather, M.W., Bhatnagar, S., Morrisey, J.M., Zhang, Z., Vaidya, A.B., Ho, C.M.

(2025) Nat Commun 16: 9092-9092

• PubMed: 41115914 
• DOI: https://doi.org/10.1038/s41467-025-64815-y
• Primary Citation of Related Structures:  
  9N10


• PubMed Abstract: 
  

  The Plasmodium falciparum sodium efflux pump PfATP4 is a leading antimalarial target, but suffers from a lack of high-resolution structural information needed to identify functionally important features in conserved regions and guide rational design of next generation inhibitors. Here, we determine a 3.7 Å cryoEM structure of PfATP4 purified from CRISPR-engineered P. falciparum parasites, revealing a previously unknown, apicomplexan-specific binding partner, PfABP, which forms a conserved, likely modulatory interaction with PfATP4. The discovery of PfABP presents an unexplored avenue for designing PfATP4 inhibitors.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA. [e-mail].
Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 161.9 kDa 
• Atom Count: 8,360 
• Modeled Residue Count: 1,064 
• Deposited Residue Count: 1,447 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-SERCA-type Ca2+ -transporting P-ATPase	A	1,264	Plasmodium falciparum Dd2	Mutation(s): 0  EC: 7.2.2.3
UniProt
Find proteins for Q9U445 (Plasmodium falciparum) Explore Q9U445  Go to UniProtKB:  Q9U445

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PfATP4 Binding Protein (PfABP)	B	183	Plasmodium falciparum Dd2	Mutation(s): 0
UniProt
Find proteins for Q8IEF9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IEF9  Go to UniProtKB:  Q8IEF9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Haile, M.T., Zhen, J., Ho, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/Office of the Director	United States	DP5OD029613

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release
  
• Version 1.1: 2025-11-05
  Changes: Data collection, Database references