9N89 | pdb_00009n89

Crystal structure of 2A2 malarial antibody

• PDB DOI: https://doi.org/10.2210/pdb9N89/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-02-07 Released: 2025-10-15 
• Deposition Author(s): Yoo, R., Julien, J.P.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: in silico

Literature

Cryo-EM structure of endogenous Pfs230:Pfs48/45 complex with six antibodies reveals mechanisms of malaria transmission-blocking activity.

Bekkering, E.T., Yoo, R., Hailemariam, S., Heide, F., Ivanochko, D., Jackman, M., Proellochs, N.I., Stoter, R., van Gemert, G.J., Maeda, A., Yuguchi, T., Wanders, O.T., van Daalen, R.C., Inklaar, M.R., Andrade, C.M., Jansen, P.W.T.C., Vermeulen, M., Bousema, T., Takashima, E., Rubinstein, J.L., Kooij, T.W.A., Jore, M.M., Julien, J.P.

(2025) Immunity 58: 2899

• PubMed: 41072404 
• DOI: https://doi.org/10.1016/j.immuni.2025.09.014
• Primary Citation of Related Structures:  
  9N5I, 9N6U, 9N7K, 9N89


• PubMed Abstract: 
  

  The Pfs230:Pfs48/45 complex forms the basis for leading malaria transmission-blocking vaccine candidates, yet little is known about its molecular assembly. Here, we used cryo-electron microscopy to elucidate the structure of the endogenous Pfs230:Pfs48/45 complex bound to six transmission-blocking antibodies. Our structure revealed that Pfs230 consists of multiple domain clusters rigidified by interactions mediated through insertion domains. Membrane-anchored Pfs48/45 formed a disk-like structure, interacting with a short C-terminal peptide on Pfs230 that was critical for Pfs230 membrane-retention in vivo. Membrane retention through this interaction was not essential for transmission to mosquitoes, suggesting that complex disruption is not a mode of action for transmission-blocking antibodies. Analyses of Pfs48/45- and Pfs230-targeted antibodies identified conserved epitopes on the Pfs230:Pfs48/45 complex and provided a structural paradigm for complement-dependent activity of Pfs230-targeting antibodies. Altogether, the antibody-bound Pfs230:Pfs48/45 structure improves our molecular understanding of this biological complex, informing the development of next-generation Plasmodium falciparum transmission-blocking interventions.

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Organizational Affiliation: 
• Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan.
Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands; Division of Molecular Genetics, the Netherlands Cancer Institute, Amsterdam, the Netherlands.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands. Electronic address: [e-mail].
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 47.11 kDa 
• Atom Count: 3,708 
• Modeled Residue Count: 427 
• Deposited Residue Count: 437 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2A2 Heavy Chain	A [auth H]	223	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2A2 Kappa Chain	B [auth L]	214	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.974	α = 90
b = 76.682	β = 90
c = 91.872	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Yoo, R., Julien, J.P.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release
  
• Version 1.1: 2025-10-22
  Changes: Database references
• Version 1.2: 2025-11-26
  Changes: Database references