9BJH | pdb_00009bjh

Crystal structure of neutralizing human monoclonal antibody 75C8 in complex with AMA1 DI-DII

• PDB DOI: https://doi.org/10.2210/pdb9BJH/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Plasmodium falciparum 3D7, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-04-25 Released: 2025-03-12 
• Deposition Author(s): Patel, P.N., Tang, W.K., Tolia, N.H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Models: experimental

Literature

A strain-transcending anti-AMA1 human monoclonal antibody neutralizes malaria parasites independent of direct RON2L receptor blockade.

Patel, P.N., Diouf, A., Dickey, T.H., Tang, W.K., Hopp, C.S., Traore, B., Long, C.A., Miura, K., Crompton, P.D., Tolia, N.H.

(2025) Cell Rep Med 6: 101985-101985

• PubMed: 40020675 
• DOI: https://doi.org/10.1016/j.xcrm.2025.101985
• Primary Citation of Related Structures:  
  9BJG, 9BJH


• PubMed Abstract: 
  

  Plasmodium falciparum apical membrane antigen 1 (AMA1) binds a loop in rhoptry neck protein 2 (RON2L) during red cell invasion and is a target for vaccines and therapeutic antibodies against malaria. Here, we report a panel of AMA1-specific naturally acquired human monoclonal antibodies (hmAbs) derived from individuals living in malaria-endemic regions. Two neutralizing hmAbs engage AMA1 independent of the RON2L-binding site. The hmAb 75B10 demonstrates potent strain-transcending neutralization that is independent of RON2L blockade, emphasizing that epitopes outside the RON2L-binding site elicit broad protection against variant parasite strains. The combination of these hmAbs synergistically enhances parasite neutralization. Vaccination with a structure-based design (SBD1) that mimics the AMA1-RON2L complex elicited antibodies similar to the two neutralizing hmAbs connecting vaccination to naturally acquired immunity in humans. The structural definition of a strain-transcending epitope on AMA1 targeted by naturally acquired hmAb establishes paradigms for developing AMA1-based vaccines and therapeutic antibodies.

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Organizational Affiliation: 
• Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
Malaria Research and Training Centre, Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Point G, Bamako 1805, Mali.
Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 179 kDa 
• Atom Count: 11,236 
• Modeled Residue Count: 1,437 
• Deposited Residue Count: 1,608 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apical membrane antigen 1	A, B	347	Plasmodium falciparum 3D7	Mutation(s): 5  Gene Names: PF3D7_1133400
UniProt
Find proteins for P22621 (Plasmodium falciparum (isolate FC27 / Papua New Guinea)) Explore P22621  Go to UniProtKB:  P22621

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
75C8 Fab Heavy Chain	C [auth H], D [auth I]	239	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
75C8 Fab Light Chain	E [auth L], F [auth M]	218	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.868	α = 94.105
b = 71.62	β = 99.195
c = 132.927	γ = 112.393

Software Package:

Software Name	Purpose
SERGUI	data collection
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Patel, P.N., Tang, W.K., Tolia, N.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1ZIAAAI001236

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Database references
• Version 1.2: 2025-04-02
  Changes: Database references