6WN1

Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 241242


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Naturally acquired blocking human monoclonal antibodies to Plasmodium vivax reticulocyte binding protein 2b.

Chan, L.J.Gandhirajan, A.Carias, L.L.Dietrich, M.H.Vadas, O.Visentin, R.Franca, C.T.Menant, S.Soldati-Favre, D.Mueller, I.King, C.L.Tham, W.H.

(2021) Nat Commun 12: 1538-1538

  • DOI: https://doi.org/10.1038/s41467-021-21811-2
  • Primary Citation of Related Structures:  
    6WM9, 6WN1, 6WNO, 6WOZ, 6WQO, 6WTU, 6WTV, 6WTY

  • PubMed Abstract: 

    Plasmodium vivax preferentially invades reticulocytes and recognition of these cells is mediated by P. vivax Reticulocyte Binding Protein 2b (PvRBP2b) binding to human Transferrin receptor 1 (TfR1) and Transferrin (Tf). Longitudinal cohort studies in Papua New Guinea, Thailand and Brazil show that PvRBP2b antibodies are correlated with protection against P. vivax infection and disease. Here, we isolate and characterize anti-PvRBP2b human monoclonal antibodies from two individuals in Cambodia with natural P. vivax infection. These antibodies bind with high affinities and map to different regions of PvRBP2b. Several human antibodies block PvRBP2b binding to reticulocytes and inhibit complex formation with human TfR1-Tf. We describe different structural mechanisms for functional inhibition, including either steric hindrance with TfR1-Tf or the reticulocyte membrane. These results show that naturally acquired human antibodies against PvRBP2b can inhibit its function which is important for P. vivax invasion.


  • Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reticulocyte binding protein 2bA,
E [auth D]
307Plasmodium 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K736
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
241242 Fab heavy chainB,
F [auth E]
237Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
241242 Fab light chainC,
D [auth F]
219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 360.698α = 90
b = 43.699β = 101.69
c = 115.332γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1160042
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1143187
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1154937
Wellcome TrustAustralia208693/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description