9DX6

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

• PDB DOI: https://doi.org/10.2210/pdb9DX6/pdb

• Classification: CELL INVASION
• Organism(s): Plasmodium vivax, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-10-10 Released: 2024-11-13 
• Deposition Author(s): Dietrich, M.H., Tham, W.H., Jung, N.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Veterans Affairs (VA, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Models: experimental

Literature

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

King, C.L., 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., Sattabongkot, J., Tham, W.-H., Popovici, J., Beeson, J.G., Bosch, J., Kirtley, P., Nielson, K., Aleshnick, M., Zanghi, G., Rezakhani, N., Vaughan, A.M., Wilder, B.K.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 102.9 kDa 
• Atom Count: 6,654 
• Modelled Residue Count: 840 
• Deposited Residue Count: 921 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apical merozoite protein 1	A	471	Plasmodium vivax	Mutation(s): 3  Gene Names: ama1
UniProt
Find proteins for B9TXF7 (Plasmodium vivax) Explore B9TXF7  Go to UniProtKB:  B9TXF7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
826827 Fab Heavy chain	B	234	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
826827 Fab Light chain	C	216	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.237	α = 90
b = 54.461	β = 97.2
c = 104.13	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Dietrich, M.H., Tham, W.H., Jung, N.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI143694
Department of Veterans Affairs (VA, United States)	United States	BX001350

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release