9DX6 | pdb_00009dx6

Crystal structure of Plasmodium vivax (Palo Alto) PvAMA1 in complex with human Fab 826827


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Potent AMA1-specific human monoclonal antibody against Plasmodium vivax Pre-erythrocytic and Blood Stages.

Winnicki, A.C.Dietrich, M.H.Yeoh, L.M.Carias, L.L.Roobsoong, W.Drago, C.L.Malachin, A.N.Redinger, K.R.Feufack-Donfack, L.B.Baldor, L.Jung, N.C.McLaine, O.S.Skomorovska-Prokvolit, Y.Orban, A.Opi, D.H.Kirtley, P.Nielson, K.Aleshnick, M.Zanghi, G.Rezakhani, N.Vaughan, A.M.Wilder, B.K.Sattabongkot, J.Tham, W.H.Popovici, J.Beeson, J.G.Bosch, J.King, C.L.

(2024) Nat Commun 15: 10556-10556

  • DOI: https://doi.org/10.1038/s41467-024-53848-4
  • Primary Citation of Related Structures:  
    9DX6

  • PubMed Abstract: 

    New therapeutics are necessary for preventing Plasmodium vivax malaria due to easy transmissibility and dormancy in the liver that increases the clinical burden due to recurrent relapse. In this manuscript we characterize 12 Pv Apical Membrane Antigen 1 (PvAMA1) specific human monoclonal antibodies from Peripheral Blood Mononuclear Cells of a Pv-exposed individual. PvAMA1 is essential for sporozoite and merozoite invasion, making it a unique therapeutic target. We show that humAb 826827 blocks the invasion of human reticulocytes using Pv clinical isolates and inhibits sporozoite invasion of human hepatocytes in vitro (IC 50 of 0.3 - 3.7 µg/mL). Inoculation of human liver transgenic (FRG-humHep) female mice with humAb 826827 significantly reduces liver infection in vivo. The crystal structure of rPvAMA1 bound to 826827 shows that 826827 partially occupies the highly conserved hydrophobic groove in PvAMA1 that binds its known receptor, RON2. We have isolated a potent humAb that is isolate-transcendent, blocks both pre-erythrocytic and blood stage infection, and could be a potential therapy for Pv.


  • Organizational Affiliation

    Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apical merozoite protein 1471Plasmodium vivaxMutation(s): 3 
Gene Names: ama1
UniProt
Find proteins for B9TXF7 (Plasmodium vivax)
Explore B9TXF7 
Go to UniProtKB:  B9TXF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9TXF7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
826827 Fab Heavy chain234Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
826827 Fab Light chain216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.237α = 90
b = 54.461β = 97.2
c = 104.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI143694
Department of Veterans Affairs (VA, United States)United StatesBX001350

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references