7UNY

Crystal structure of D2 nanobody in complex with PfCSS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.13 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Literature

PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum.

Scally, S.W.Triglia, T.Evelyn, C.Seager, B.A.Pasternak, M.Lim, P.S.Healer, J.Geoghegan, N.D.Adair, A.Tham, W.H.Dagley, L.F.Rogers, K.L.Cowman, A.F.

(2022) Nat Microbiol 7: 2039-2053

  • DOI: https://doi.org/10.1038/s41564-022-01261-2
  • Primary Citation of Related Structures:  
    7UNY, 7UNZ

  • PubMed Abstract: 

    The most severe form of malaria is caused by Plasmodium falciparum. These parasites invade human erythrocytes, and an essential step in this process involves the ligand PfRh5, which forms a complex with cysteine-rich protective antigen (CyRPA) and PfRh5-interacting protein (PfRipr) (RCR complex) and binds basigin on the host cell. We identified a heteromeric disulfide-linked complex consisting of P. falciparum Plasmodium thrombospondin-related apical merozoite protein (PfPTRAMP) and P. falciparum cysteine-rich small secreted protein (PfCSS) and have shown that it binds RCR to form a pentameric complex, PCRCR. Using P. falciparum lines with conditional knockouts, invasion inhibitory nanobodies to both PfPTRAMP and PfCSS, and lattice light-sheet microscopy, we show that they are essential for merozoite invasion. The PCRCR complex functions to anchor the contact between merozoite and erythrocyte membranes brought together by strong parasite deformations. We solved the structure of nanobody-PfCSS complexes to identify an inhibitory epitope. Our results define the function of the PCRCR complex and identify invasion neutralizing epitopes providing a roadmap for structure-guided development of these proteins for a blood stage malaria vaccine.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine-rich small secreted protein CSSA,
B [auth D]
289Plasmodium falciparumMutation(s): 1 
Gene Names: PF3D7_1404700
UniProt
Find proteins for Q8IM47 (Plasmodium falciparum (isolate 3D7))
Explore Q8IM47 
Go to UniProtKB:  Q8IM47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IM47
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D2 NanobodyC [auth B],
D [auth C]
130Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, H, J
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.13 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.416α = 90
b = 182.416β = 90
c = 143.728γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia637406
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1173049

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description