6BPA

Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 3E9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of an essential Plasmodium vivax invasion complex.

Gruszczyk, J.Huang, R.K.Chan, L.J.Menant, S.Hong, C.Murphy, J.M.Mok, Y.F.Griffin, M.D.W.Pearson, R.D.Wong, W.Cowman, A.F.Yu, Z.Tham, W.H.

(2018) Nature 559: 135-139

  • DOI: 10.1038/s41586-018-0249-1
  • Primary Citation of Related Structures:  
    6BPA, 6BPC, 6BPB, 6BPE, 6BPD, 6D03, 6D05, 6D04

  • PubMed Abstract: 
  • Plasmodium vivax is the most widely distributed malaria parasite that infects humans 1 . P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1) 2 ...

    Plasmodium vivax is the most widely distributed malaria parasite that infects humans 1 . P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1) 2 . TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates 2 . Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 Å resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.


    Organizational Affiliation

    Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia. tham@wehi.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reticulocyte binding protein 2, putativeA, D307Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_094255
UniProt
Find proteins for A5K736 (Plasmodium vivax (strain Salvador I))
Explore A5K736 
Go to UniProtKB:  A5K736
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody 3E9 Fab heavy chainB, E256Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody 3E9 Fab light chainC, F236Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
G [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.07α = 90
b = 177.1β = 90
c = 178.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection, Database references