6D05

Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: https://doi.org/10.1038/s41586-018-0249-1
  • Primary Citation of Related Structures:  
    6BPA, 6BPB, 6BPC, 6BPD, 6BPE, 6D03, 6D04, 6D05

  • 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 . 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

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transferrin receptor protein 1
A, B
659Homo sapiensMutation(s): 1 
Gene Names: TFRC
UniProt & NIH Common Fund Data Resources
Find proteins for P02786 (Homo sapiens)
Explore P02786 
Go to UniProtKB:  P02786
PHAROS:  P02786
GTEx:  ENSG00000072274 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02786
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P02786-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serotransferrin
C, D
698Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens)
Explore P02787 
Go to UniProtKB:  P02787
PHAROS:  P02787
GTEx:  ENSG00000091513 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02787
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P02787-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reticulocyte binding protein 2, putative
E, F
820Plasmodium vivax Sal-1Mutation(s): 1 
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
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K
G, H, I, J, K, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
N [auth A],
P [auth B],
U [auth C],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
R [auth C],
T [auth C],
W [auth D],
Y [auth D]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
Q [auth C],
S [auth C],
V [auth D],
X [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth A],
O [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.12-2829
RECONSTRUCTIONRELION

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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary