8RXO | pdb_00008rxo

ACDC domain of Plasmodium falciparum AP2-I transcription factor

• PDB DOI: https://doi.org/10.2210/pdb8RXO/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-07 Released: 2024-03-06 
• Deposition Author(s): Nessler, S., Le Berre, M., Li De La Sierra, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: in silico

Literature

Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against apicomplexan parasites.

Le Berre, M., Tubiana, T., Reutersward Waldner, P., Lazar, N., Li de la Sierra-Gallay, I., Santos, J.M., Llinas, M., Nessler, S.

(2025) Acta Crystallogr D Struct Biol 81: 38-48

• PubMed: 39820027 
• DOI: https://doi.org/10.1107/S2059798324012518
• Primary Citation of Related Structures:  
  8RWU, 8RXA, 8RXO


• PubMed Abstract: 
  

  The apicomplexan AP2 (ApiAP2) proteins are the best characterized family of DNA-binding proteins in Plasmodium spp. malaria parasites. Apart from the AP2 DNA-binding domain, there is little sequence similarity between ApiAP2 proteins. However, a conserved AP2-coincident domain mostly at the C-terminus (ACDC domain) is observed in a subset of the ApiAP2 proteins. The structure and function of this domain remain unknown. We report two crystal structures of ACDC domains derived from distinct Plasmodium ApiAP2 proteins, revealing a conserved, unique, noncanonical, four-helix bundle architecture. We used these structures to perform in silico docking calculations against a library of known antimalarial compounds and identified potential small-molecule ligands that bind in a highly conserved hydrophobic pocket that is present in all apicomplexan ACDC domains. These ligands provide a new molecular basis for the future design of ACDC inhibitors.

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Organizational Affiliation: 
• Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.3 kDa 
• Atom Count: 1,546 
• Modeled Residue Count: 194 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP2 domain transcription factor AP2-I	A, B	152	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF3D7_1007700
UniProt
Find proteins for Q8IJW6 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJW6  Go to UniProtKB:  Q8IJW6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.237 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.08	α = 90
b = 78.08	β = 90
c = 127.84	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Nessler, S., Le Berre, M., Li De La Sierra, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release
  
• Version 2.0: 2024-12-25
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary
• Version 2.1: 2025-01-22
  Changes: Data collection, Database references
• Version 2.2: 2025-01-29
  Changes: Database references