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- EMDB-3123: A Spiral Scaffold Underlies Cytoadherent Knobs in Plasmodium falc... -

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Basic information

Entry
Database: EMDB / ID: EMD-3123
TitleA Spiral Scaffold Underlies Cytoadherent Knobs in Plasmodium falciparum-Infected Erythrocytes
Map dataTomogram of negative-stained Plasmodium falciparum schizont skeleton
Sample
  • Sample: Detergent-insoluble skeleton of Plasmodium falciparum schizont
  • Organelle or cellular component: cytoskeleton
Keywordsmalaria / Plasmodium / knobs / cytoadherence / KAHRP / erythrocyte / skeleton / schizont / blood
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodelectron tomography
AuthorsWatermeyer JM / Hale VL / Hackett F / Clare DK / Cutts EE / Vakonakis I / Fleck RA / Blackman MJ / Saibil HR
CitationJournal: Blood / Year: 2016
Title: A spiral scaffold underlies cytoadherent knobs in Plasmodium falciparum-infected erythrocytes.
Authors: Jean M Watermeyer / Victoria L Hale / Fiona Hackett / Daniel K Clare / Erin E Cutts / Ioannis Vakonakis / Roland A Fleck / Michael J Blackman / Helen R Saibil /
Abstract: Much of the virulence of Plasmodium falciparum malaria is caused by cytoadherence of infected erythrocytes, which promotes parasite survival by preventing clearance in the spleen. Adherence is ...Much of the virulence of Plasmodium falciparum malaria is caused by cytoadherence of infected erythrocytes, which promotes parasite survival by preventing clearance in the spleen. Adherence is mediated by membrane protrusions known as knobs, whose formation depends on the parasite-derived, knob-associated histidine-rich protein (KAHRP). Knobs are required for cytoadherence under flow conditions, and they contain both KAHRP and the parasite-derived erythrocyte membrane protein PfEMP1. Using electron tomography, we have examined the 3-dimensional structure of knobs in detergent-insoluble skeletons of P falciparum 3D7 schizonts. We describe a highly organized knob skeleton composed of a spiral structure coated by an electron-dense layer underlying the knob membrane. This knob skeleton is connected by multiple links to the erythrocyte cytoskeleton. We used immuno-electron microscopy (EM) to locate KAHRP in these structures. The arrangement of membrane proteins in the knobs, visualized by high-resolution freeze-fracture scanning EM, is distinct from that in the surrounding erythrocyte membrane, with a structure at the apex that likely represents the adhesion site. Thus, erythrocyte knobs in P falciparum infection contain a highly organized skeleton structure underlying a specialized region of membrane. We propose that the spiral and dense coat organize the cytoadherence structures in the knob, and anchor them into the erythrocyte cytoskeleton. The high density of knobs and their extensive mechanical linkage suggest an explanation for the rigidification of the cytoskeleton in infected cells, and for the transmission to the cytoskeleton of shear forces experienced by adhering cells.
History
DepositionAug 11, 2015-
Header (metadata) releaseAug 26, 2015-
Map releaseDec 23, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3123.tif

Downloads & links

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Map

FileDownload / File: emd_3123.map.gz / Format: CCP4 / Size: 302.7 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationTomogram of negative-stained Plasmodium falciparum schizont skeleton
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.85 Å/pix.
x 44 pix.
= 301.532 Å		6.85 Å/pix.
x 1938 pix.
= 13281.114 Å		6.85 Å/pix.
x 1906 pix.
= 13061.818 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.853 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0.0 - 32767.0
Average (Standard dev.)14431.108398439999291 (±3204.112304690000201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0022
Dimensions1938190644
Spacing1938190644
CellA: 13061.818 Å / B: 13281.114 Å / C: 301.532 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z6.8536.8536.853
M x/y/z1906193844
origin x/y/z0.0000.0000.000
length x/y/z13061.81813281.114301.532
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS0022
NC/NR/NS1906193844
D min/max/mean0.00032767.00014431.108

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Supplemental data

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Sample components

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Entire : Detergent-insoluble skeleton of Plasmodium falciparum schizont

EntireName: Detergent-insoluble skeleton of Plasmodium falciparum schizont
Components
  • Sample: Detergent-insoluble skeleton of Plasmodium falciparum schizont
  • Organelle or cellular component: cytoskeleton

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Supramolecule #1000: Detergent-insoluble skeleton of Plasmodium falciparum schizont

SupramoleculeName: Detergent-insoluble skeleton of Plasmodium falciparum schizont
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: cytoskeleton

SupramoleculeName: cytoskeleton / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / synonym: malaria parasite / Location in cell: erythrocyte cytoskeleton

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Experimental details

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Structure determination

Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridDetails: 300 mesh copper grid with lacy carbon film and thin carbon overlay
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
DateMar 7, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 260 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 68 ° / Tilt series - Axis1 - Angle increment: 2 °

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Image processing

Detailsdual-axis tomogram
Final reconstructionSoftware - Name: IMOD / Number images used: 140

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