Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.04 kDa 
• Atom Count: 6227 
• Modelled Residue Count: 747 
• Deposited Residue Count: 762 
• Unique protein chains: 1

4XBI

Structure Of A Malarial Protein Involved in Proteostasis

• PDB DOI: 10.2210/pdb4XBI/pdb

• Classification: CHAPERONE
• Organism(s): Plasmodium falciparum 3D7, Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-17 Released: 2015-07-29 
• Deposition Author(s): Egea, P.F., Ah Young, A.P., Cascio, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design.

AhYoung, A.P., Koehl, A., Cascio, D., Egea, P.F.

(2015) Protein Sci 24: 1508-1520

• PubMed: 26130467 
• DOI: 10.1002/pro.2739
• Primary Citation of Related Structures:  
  4IOD, 4IRF, 4XBI


• PubMed Abstract: 
  

Caseinolytic chaperones and proteases (Clp) belong to the AAA+ protein superfamily and are part of the protein quality control machinery in cells. The eukaryotic parasite Plasmodium falciparum, the causative agent of malaria, has evolved an elaborate network of Clp proteins including two distinct ClpB ATPases. ClpB1 and ClpB2 are involved in different aspects of parasitic proteostasis. ClpB1 is present in the apicoplast, a parasite-specific and plastid-like organelle hosting various metabolic pathways necessary for parasite growth. ClpB2 localizes to the parasitophorous vacuole membrane where it drives protein export as core subunit of a parasite-derived protein secretion complex, the Plasmodium Translocon of Exported proteins (PTEX); this process is central to parasite virulence and survival in the human host. The functional associations of these two chaperones with parasite-specific metabolism and protein secretion make them prime drug targets. ClpB proteins function as unfoldases and disaggregases and share a common architecture consisting of four domains-a variable N-terminal domain that binds different protein substrates, followed by two highly conserved catalytic ATPase domains, and a C-terminal domain. Here, we report and compare the first crystal structures of the N terminal domains of ClpB1 and ClpB2 from Plasmodium and analyze their molecular surfaces. Solution scattering analysis of the N domain of ClpB2 shows that the average solution conformation is similar to the crystalline structure. These structures represent the first step towards the characterization of these two malarial chaperones and the reconstitution of the entire PTEX to aid structure-based design of novel anti-malarial drugs.

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Organizational Affiliation: 

Molecular Biology Institute, UCLA, Los Angeles, California.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ClpB protein, putative,Green fluorescent protein	A, B	381	Plasmodium falciparum 3D7, Aequorea victoria This entity is chimeric	Mutation(s): 12  Gene Names: PF08_0063, GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for Q8IB03 (Plasmodium falciparum (isolate 3D7)) Explore Q8IB03  Go to UniProtKB:  Q8IB03
UniProt Groups	P42212Q8IB03

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO	A, B	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.53	α = 90
b = 127.53	β = 90
c = 92.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-17 
• Released Date: 2015-07-29 
Deposition Author(s): Egea, P.F., Ah Young, A.P., Cascio, D.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references