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- EMDB-9193: Structure of Plasmodium falciparum CyRPA/Ripr invasion complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9193
TitleStructure of Plasmodium falciparum CyRPA/Ripr invasion complex
Map dataCryo-electron microscopy structure of Plasmodium falciparum CyRPA/PfRipr complex
Sample
  • Complex: CyRPR/PfRipr complex
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.07 Å
AuthorsWilson W / Alan C / Zhiheng Y
CitationJournal: Nature / Year: 2019
Title: Structure of Plasmodium falciparum Rh5-CyRPA-Ripr invasion complex.
Authors: Wilson Wong / Rick Huang / Sebastien Menant / Chuan Hong / Jarrod J Sandow / Richard W Birkinshaw / Julie Healer / Anthony N Hodder / Usheer Kanjee / Christopher J Tonkin / Denise Heckmann / ...Authors: Wilson Wong / Rick Huang / Sebastien Menant / Chuan Hong / Jarrod J Sandow / Richard W Birkinshaw / Julie Healer / Anthony N Hodder / Usheer Kanjee / Christopher J Tonkin / Denise Heckmann / Vladislav Soroka / Teit Max Moscote Søgaard / Thomas Jørgensen / Manoj T Duraisingh / Peter E Czabotar / Willem A de Jongh / Wai-Hong Tham / Andrew I Webb / Zhiheng Yu / Alan F Cowman /
Abstract: Plasmodium falciparum causes the severe form of malaria that has high levels of mortality in humans. Blood-stage merozoites of P. falciparum invade erythrocytes, and this requires interactions ...Plasmodium falciparum causes the severe form of malaria that has high levels of mortality in humans. Blood-stage merozoites of P. falciparum invade erythrocytes, and this requires interactions between multiple ligands from the parasite and receptors in hosts. These interactions include the binding of the Rh5-CyRPA-Ripr complex with the erythrocyte receptor basigin, which is an essential step for entry into human erythrocytes. Here we show that the Rh5-CyRPA-Ripr complex binds the erythrocyte cell line JK-1 significantly better than does Rh5 alone, and that this binding occurs through the insertion of Rh5 and Ripr into host membranes as a complex with high molecular weight. We report a cryo-electron microscopy structure of the Rh5-CyRPA-Ripr complex at subnanometre resolution, which reveals the organization of this essential invasion complex and the mode of interactions between members of the complex, and shows that CyRPA is a critical mediator of complex assembly. Our structure identifies blades 4-6 of the β-propeller of CyRPA as contact sites for Rh5 and Ripr. The limited contacts between Rh5-CyRPA and CyRPA-Ripr are consistent with the dissociation of Rh5 and Ripr from CyRPA for membrane insertion. A comparision of the crystal structure of Rh5-basigin with the cryo-electron microscopy structure of Rh5-CyRPA-Ripr suggests that Rh5 and Ripr are positioned parallel to the erythrocyte membrane before membrane insertion. This provides information on the function of this complex, and thereby provides insights into invasion by P. falciparum.
History
DepositionOct 8, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseDec 19, 2018-
UpdateDec 19, 2018-
Current statusDec 19, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.36
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9193.png

Downloads & links

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Map

FileDownload / File: emd_9193.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron microscopy structure of Plasmodium falciparum CyRPA/PfRipr complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.36 / Movie #1: 4.36
Minimum - Maximum-8.836411999999999 - 16.274643000000001
Average (Standard dev.)0.01262244 (±0.6097192)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-8.83616.2750.013

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Supplemental data

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Sample components

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Entire : CyRPR/PfRipr complex

EntireName: CyRPR/PfRipr complex
Components
  • Complex: CyRPR/PfRipr complex

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Supramolecule #1: CyRPR/PfRipr complex

SupramoleculeName: CyRPR/PfRipr complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Recombinant expressionOrganism: unidentified baculovirus
Molecular weightTheoretical: 163 kDa/nm

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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: 8.5 / Details: 20 mM Tris, pH8.5 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was equipped with a Cs corrector with two hexapole elements
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 4 / Number real images: 12974 / Average exposure time: 10.0 sec. / Average electron dose: 92.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 48077 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initial
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 533180
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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