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- EMDB-16639: PfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16639
TitlePfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to antibody Cy.003 - local refinement on PfRIPR
Map datalocal refinement on PfRIPR after DeepEMhancer
Sample
  • Complex: PfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to antibody Cy.003
Keywordsmalaria / erythrocyte invasion / Plasmodium falciparum / CELL ADHESION
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsFarrell B / Higgins MK
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust220797/Z/20/Z United Kingdom
CitationJournal: Nature / Year: 2024
Title: The PfRCR complex bridges malaria parasite and erythrocyte during invasion.
Authors: Brendan Farrell / Nawsad Alam / Melissa N Hart / Abhishek Jamwal / Robert J Ragotte / Hannah Walters-Morgan / Simon J Draper / Ellen Knuepfer / Matthew K Higgins /
Abstract: The symptoms of malaria occur during the blood stage of infection, when parasites invade and replicate within human erythrocytes. The PfPCRCR complex, containing PfRH5 (refs. ), PfCyRPA, PfRIPR, ...The symptoms of malaria occur during the blood stage of infection, when parasites invade and replicate within human erythrocytes. The PfPCRCR complex, containing PfRH5 (refs. ), PfCyRPA, PfRIPR, PfCSS and PfPTRAMP, is essential for erythrocyte invasion by the deadliest human malaria parasite, Plasmodium falciparum. Invasion can be prevented by antibodies or nanobodies against each of these conserved proteins, making them the leading blood-stage malaria vaccine candidates. However, little is known about how PfPCRCR functions during invasion. Here we present the structure of the PfRCR complex, containing PfRH5, PfCyRPA and PfRIPR, determined by cryogenic-electron microscopy. We test the hypothesis that PfRH5 opens to insert into the membrane, instead showing that a rigid, disulfide-locked PfRH5 can mediate efficient erythrocyte invasion. We show, through modelling and an erythrocyte-binding assay, that PfCyRPA-binding antibodies neutralize invasion through a steric mechanism. We determine the structure of PfRIPR, showing that it consists of an ordered, multidomain core flexibly linked to an elongated tail. We also show that the elongated tail of PfRIPR, which is the target of growth-neutralizing antibodies, binds to the PfCSS-PfPTRAMP complex on the parasite membrane. A modular PfRIPR is therefore linked to the merozoite membrane through an elongated tail, and its structured core presents PfCyRPA and PfRH5 to interact with erythrocyte receptors. This provides fresh insight into the molecular mechanism of erythrocyte invasion and opens the way to new approaches in rational vaccine design.
History
DepositionFeb 3, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16639.png

Downloads & links

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Map

FileDownload / File: emd_16639.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement on PfRIPR after DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 416 pix.
= 346.112 Å		0.83 Å/pix.
x 416 pix.
= 346.112 Å		0.83 Å/pix.
x 416 pix.
= 346.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0017993506 - 2.6886666
Average (Standard dev.)0.0001919535 (±0.009839471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 346.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16639_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: local refinement on PfRIPR

Fileemd_16639_additional_1.map
Annotationlocal refinement on PfRIPR
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: local refinement on PfRIPR - half map A

Fileemd_16639_half_map_1.map
Annotationlocal refinement on PfRIPR - half map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: local refinement on PfRIPR - half map B

Fileemd_16639_half_map_2.map
Annotationlocal refinement on PfRIPR - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to ...

EntireName: PfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to antibody Cy.003
Components
  • Complex: PfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to antibody Cy.003

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Supramolecule #1: PfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to ...

SupramoleculeName: PfRH5-PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to antibody Cy.003
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.97 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 253444

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