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- EMDB-13192: Structure of knob spiral in P. falciparum-infected erythrocytes -

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Basic information

Entry
Database: EMDB / ID: EMD-13192
TitleStructure of knob spiral in P. falciparum-infected erythrocytes
Map dataEM_map
Sample
  • Complex: Knob spiral
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsChang S-YS / Kudryashev M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
CitationJournal: Mol Microbiol / Year: 2022
Title: KAHRP dynamically relocalizes to remodeled actin junctions and associates with knob spirals in Plasmodium falciparum-infected erythrocytes.
Authors: Cecilia P Sanchez / Pintu Patra / Shih-Ying Scott Chang / Christos Karathanasis / Lukas Hanebutte / Nicole Kilian / Marek Cyrklaff / Mike Heilemann / Ulrich S Schwarz / Mikhail Kudryashev / Michael Lanzer /
Abstract: The knob-associated histidine-rich protein (KAHRP) plays a pivotal role in the pathophysiology of Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, which anchor ...The knob-associated histidine-rich protein (KAHRP) plays a pivotal role in the pathophysiology of Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, which anchor parasite-encoded adhesins to the membrane skeleton. The resulting sequestration of parasitized erythrocytes in the microvasculature leads to severe disease. Despite KAHRP being an important virulence factor, its physical location within the membrane skeleton is still debated, as is its function in knob formation. Here, we show by super-resolution microscopy that KAHRP initially associates with various skeletal components, including ankyrin bridges, but eventually colocalizes with remnant actin junctions. We further present a 35 Å map of the spiral scaffold underlying knobs and show that a KAHRP-targeting nanoprobe binds close to the spiral scaffold. Single-molecule localization microscopy detected ~60 KAHRP molecules/knob. We propose a dynamic model of KAHRP organization and a function of KAHRP in attaching other factors to the spiral scaffold.
History
DepositionJul 9, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateFeb 23, 2022-
Current statusFeb 23, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13192.png

Downloads & links

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Map

FileDownload / File: emd_13192.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM_map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.39 Å/pix.
x 360 pix.
= 1220.4 Å		3.39 Å/pix.
x 360 pix.
= 1220.4 Å		3.39 Å/pix.
x 360 pix.
= 1220.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.4 / Movie #1: 1.9
Minimum - Maximum-6.0773444 - 7.6025357
Average (Standard dev.)0.014586698 (±0.6003156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1220.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.393.393.39
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z1220.4001220.4001220.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-6.0777.6030.015

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Supplemental data

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Mask #1

Fileemd_13192_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Knob spiral

EntireName: Knob spiral
Components
  • Complex: Knob spiral

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Supramolecule #1: Knob spiral

SupramoleculeName: Knob spiral / type: complex / ID: 1 / Parent: 0 / Details: Knob spiral in P. falciparum-infected erythrocytes
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: PBS buffer
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III
DetailsP. falciparum-infected erythrocytes

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 332
ExtractionNumber tomograms: 43 / Number images used: 489 / Software - Name: Dynamo
CTF correctionSoftware - Name: Gctf
Final 3D classificationSoftware - Name: Dynamo
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: Dynamo
FSC plot (resolution estimation)

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