4WAT | pdb_00004wat

Crystal structure of PfRh5, an essential P. falciparum ligand for invasion of human erythrocytes

• PDB DOI: https://doi.org/10.2210/pdb4WAT/pdb

• Classification: CELL INVASION
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-09-01 Released: 2014-10-22 
• Deposition Author(s): Chen, L.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.247 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of PfRh5, an essential P. falciparum ligand for invasion of human erythrocytes.

Chen, L., Xu, Y., Healer, J., Thompson, J.K., Smith, B.J., Lawrence, M.C., Cowman, A.F.

(2014) Elife 3

• PubMed: 25296023 
• DOI: https://doi.org/10.7554/eLife.04187
• Primary Citation Related Structures: 
  4WAT


• PubMed Abstract: 
  

  Plasmodium falciparum causes the most severe form of malaria in humans and is responsible for over 700,000 deaths annually. It is an obligate intracellular parasite and invades erythrocytes where it grows in a relatively protected niche. Invasion of erythrocytes is essential for parasite survival and this involves interplay of multiple protein–protein interactions. One of the most important interactions is binding of parasite invasion ligand families EBLs and PfRhs to host receptors on the surface of erythrocytes. PfRh5 is the only essential invasion ligand within the PfRh family and is an important vaccine candidate. PfRh5 binds the host receptor basigin. In this study, we have determined the crystal structure of PfRh5 using diffraction data to 2.18 Å resolution. PfRh5 exhibits a novel fold, comprising nine mostly anti-parallel α-helices encasing an N-terminal β-hairpin, with the overall shape being an elliptical disk. This is the first three-dimensional structure determined for the PfRh family of proteins. DOI: http://dx.doi.org/10.7554/eLife.04187.001

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Organizational Affiliation: 
• Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.
Department of Medical Biology, University of Melbourne, Melbourne, Australia.
Department of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 48.74 kDa 
• Atom Count: 2,923 
• Modeled Residue Count: 332 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PfRh5	A	402	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: pfrh5
UniProt
Find proteins for Q8IFM5 (Plasmodium falciparum (isolate 3D7)) Explore Q8IFM5  Go to UniProtKB:  Q8IFM5
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IMD	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.247 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.98	α = 90
b = 86.26	β = 90
c = 114.83	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Chen, L.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	637406

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Data collection, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2024-10-16
  Changes: Structure summary