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Yorodumi- EMDB-3117: A Spiral Scaffold Underlies Cytoadherent Knobs in Plasmodium falc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3117 | |||||||||
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Title | A Spiral Scaffold Underlies Cytoadherent Knobs in Plasmodium falciparum-Infected Erythrocytes | |||||||||
Map data | Cryo-tomogram of uninfected erythrocyte skeleton | |||||||||
Sample |
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Keywords | malaria / Plasmodium / knobs / cytoadherence / KAHRP / erythrocyte / skeleton / schizont / blood | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Watermeyer JM / Hale VL / Hackett F / Clare DK / Cutts EE / Vakonakis I / Fleck RA / Blackman MJ / Saibil HR | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3117.map.gz | 423.5 MB | EMDB map data format | |
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Header (meta data) | emd-3117-v30.xml emd-3117.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | EMD-3117.tif | 392.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3117 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3117 | HTTPS FTP |
-Validation report
Summary document | emd_3117_validation.pdf.gz | 156.5 KB | Display | EMDB validaton report |
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Full document | emd_3117_full_validation.pdf.gz | 155.7 KB | Display | |
Data in XML | emd_3117_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3117 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3117 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3117.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-tomogram of uninfected erythrocyte skeleton | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Detergent-insoluble skeleton of human erythrocyte
Entire | Name: Detergent-insoluble skeleton of human erythrocyte |
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Components |
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-Supramolecule #1000: Detergent-insoluble skeleton of human erythrocyte
Supramolecule | Name: Detergent-insoluble skeleton of human erythrocyte / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: cytoskeleton
Supramolecule | Name: cytoskeleton / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human / Tissue: blood / Cell: erythrocyte / Location in cell: cytoskeleton |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: 300 mesh gold Quantifoil grid R3.5/1 |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: Gatan Quantum |
Details | counting mode |
Date | May 5, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 110 e/Å2 Details: Images were the average of 20 subframes recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 2 ° |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: IMOD / Number images used: 61 |
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CTF correction | Details: each image |