4Z0F

Crystal structure of FVO strain Plasmodium falciparum AMA1 in complex with the RON2hp [Phe2038(6CW)] peptide

• PDB DOI:  https://doi.org/10.2210/pdb4Z0F/pdb

• Classification: CELL INVASION
• Organism(s): Plasmodium falciparum Vietnam Oak-Knoll (FVO), Plasmodium falciparum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-26 Released: 2016-08-03 
• Deposition Author(s): Wang, G., McGowan, S., Norton, R.S., Scanlon, M.J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Structure-Activity Studies of beta-Hairpin Peptide Inhibitors of the Plasmodium falciparum AMA1-RON2 Interaction.

Wang, G., Drinkwater, N., Drew, D.R., MacRaild, C.A., Chalmers, D.K., Mohanty, B., Lim, S.S., Anders, R.F., Beeson, J.G., Thompson, P.E., McGowan, S., Simpson, J.S., Norton, R.S., Scanlon, M.J.

(2016) J Mol Biol 428: 3986-3998

• PubMed: 27422009 
• DOI: https://doi.org/10.1016/j.jmb.2016.07.001
• Primary Citation of Related Structures:  
  4Z09, 4Z0D, 4Z0E, 4Z0F


• PubMed Abstract: 
  

The interaction between apical membrane antigen 1 (AMA1) and rhoptry neck protein 2 (RON2) plays a key role in the invasion of red blood cells by Plasmodium parasites. Disruption of this critical protein-protein interaction represents a promising avenue for antimalarial drug discovery. In this work, we exploited a 13-residue β-hairpin based on the C-terminal loop of RON2 to probe a conserved binding site on Plasmodium falciparum AMA1. A series of mutations was synthetically engineered into β-hairpin peptides to establish structure-activity relationships. The best mutations improved the binding affinity of the β-hairpin peptide by ~7-fold for 3D7 AMA1 and ~14-fold for FVO AMA1. We determined the crystal structures of several β-hairpin peptides in complex with AMA1 in order to define the structural features and specific interactions that contribute to improved binding affinity. The same mutations in the longer RON2sp2 peptide (residues 2027-2055 of RON2) increased the binding affinity by >30-fold for 3D7 and FVO AMA1, producing K _D values of 2.1nM and 0.4nM, respectively. To our knowledge, this is the most potent strain-transcending peptide reported to date and represents a valuable tool to characterize the AMA1-RON2 interaction.

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Organizational Affiliation: 

Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia. 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)

Macromolecule Content

• Total Structure Weight: 39.92 kDa 
• Atom Count: 2,428 
• Modelled Residue Count: 291 
• Deposited Residue Count: 348 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apical membrane antigen 1	A	335	Plasmodium falciparum Vietnam Oak-Knoll (FVO)	Mutation(s): 0  Gene Names: PFFVO_05649
UniProt
Find proteins for A0A024UZE1 (Plasmodium falciparum Vietnam Oak-Knoll) Explore A0A024UZE1  Go to UniProtKB:  A0A024UZE1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhoptry neck protein 2	B [auth C]	13	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for Q8IKV6 (Plasmodium falciparum (isolate 3D7)) Explore Q8IKV6  Go to UniProtKB:  Q8IKV6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
6CW	B [auth C]	L-PEPTIDE LINKING	C11 H11 Cl N2 O2		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.1	α = 90
b = 72.181	β = 90
c = 115.74	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Wang, G., McGowan, S., Norton, R.S., Scanlon, M.J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1025150

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description