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- EMDB-16636: PfCyRPA-PfRIPR complex from Plasmodium falciparum bound to antibo... -

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Basic information

Entry
Database: EMDB / ID: EMD-16636
TitlePfCyRPA-PfRIPR complex from Plasmodium falciparum bound to antibody Cy.003 consensus maps
Map dataconsensus map after DeepEMhancer
Sample
  • Complex: PfCyRPA-PfRIPR complex bound to Fab fragment from antibody Cy.003
KeywordsPlasmodium falciparum / erythrocyte-invasion / PfRCR / blood stage malaria vaccine / CELL ADHESION
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 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_16636.png

Downloads & links

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Map

FileDownload / File: emd_16636.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map 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)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0018178219 - 2.0565872
Average (Standard dev.)0.00043863707 (±0.014688259)
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_16636_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: consensus map

Fileemd_16636_additional_1.map
Annotationconsensus map
Projections & Slices
AxesZYX

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Half map: consensus map - half map A

Fileemd_16636_half_map_1.map
Annotationconsensus map - half map A
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: consensus map - half map B

Fileemd_16636_half_map_2.map
Annotationconsensus map - half map B
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PfCyRPA-PfRIPR complex bound to Fab fragment from antibody Cy.003

EntireName: PfCyRPA-PfRIPR complex bound to Fab fragment from antibody Cy.003
Components
  • Complex: PfCyRPA-PfRIPR complex bound to Fab fragment from antibody Cy.003

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Supramolecule #1: PfCyRPA-PfRIPR complex bound to Fab fragment from antibody Cy.003

SupramoleculeName: PfCyRPA-PfRIPR complex bound to Fab fragment from antibody Cy.003
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.97 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 506797
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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