3HGF

Expression, purification, spectroscopical and crystallographical studies of segments of the nucleotide binding domain of the reticulocyte binding protein Py235 of Plasmodium yoelii

• PDB DOI: https://doi.org/10.2210/pdb3HGF/pdb

• Classification: NUCLEOTIDE BINDING PROTEIN
• Organism(s): Plasmodium yoelii yoelii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-13 Released: 2010-02-23 
• Deposition Author(s): Gruber, A., Manimekalai, M.S.S., Balakrishna, A.M., Hunke, C., Jeyakanthan, J., Preiser, P.R., Gruber, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.373 
• R-Value Work: 0.339 
• R-Value Observed: 0.349 

Literature

Structural determination of functional units of the nucleotide binding domain (NBD94) of the reticulocyte binding protein Py235 of Plasmodium yoelii

Gruber, A., Manimekalai, M.S.S., Balakrishna, A.M., Hunke, C., Jeyakanthan, J., Preiser, P.R., Gruber, G.

(2010) PLoS One 5: e9146-e9146

• PubMed: 20161776 
• DOI: https://doi.org/10.1371/journal.pone.0009146
• Primary Citation of Related Structures:  
  3HGF


• PubMed Abstract: 
  

  Invasion of the red blood cells (RBC) by the merozoite of malaria parasites involves a large number of receptor ligand interactions. The reticulocyte binding protein homologue family (RH) plays an important role in erythrocyte recognition as well as virulence. Recently, it has been shown that members of RH in addition to receptor binding may also have a role as ATP/ADP sensor. A 94 kDa region named Nucleotide-Binding Domain 94 (NBD94) of Plasmodium yoelii YM, representative of the putative nucleotide binding region of RH, has been demonstrated to bind ATP and ADP selectively. Binding of ATP or ADP induced nucleotide-dependent structural changes in the C-terminal hinge-region of NBD94, and directly impacted on the RBC binding ability of RH.

---

Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University, Singapore. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.61 kDa 
• Atom Count: 1,375 
• Modelled Residue Count: 274 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhoptry protein fragment	A, B, C	107	Plasmodium yoelii yoelii	Mutation(s): 0  Gene Names: Plasmodium yoelii gene
UniProt
Find proteins for Q7RPU0 (Plasmodium yoelii yoelii) Explore Q7RPU0  Go to UniProtKB:  Q7RPU0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.373 
• R-Value Work: 0.339 
• R-Value Observed: 0.349 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.223	α = 90
b = 70.223	β = 90
c = 193.218	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Gruber, A., Manimekalai, M.S.S., Balakrishna, A.M., Hunke, C., Jeyakanthan, J., Preiser, P.R., Gruber, G.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-22
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references