6D04

Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • PubMed Abstract: 
  • Plasmodium vivax is the most widely distributed malaria parasite that infects humans <sup>1 </sup>. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b ...

    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

    CryoEM Shared Resource, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. tham@wehi.edu.au.,CryoEM Shared Resource, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. yuz@janelia.hhmi.org.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia. tham@wehi.edu.au.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transferrin receptor protein 1
A, B
659Homo sapiensMutation(s): 0 
Gene Names: TFRC
Find proteins for P02786 (Homo sapiens)
Go to Gene View: TFRC
Go to UniProtKB:  P02786
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serotransferrin
C, D
698Homo sapiensMutation(s): 0 
Gene Names: TF
Find proteins for P02787 (Homo sapiens)
Go to Gene View: TF
Go to UniProtKB:  P02787
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reticulocyte binding protein 2, putative
E, F
820Plasmodium vivax (strain Salvador I)Mutation(s): 0 
Find proteins for A5K736 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K736
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
C, D
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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