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Yorodumi- EMDB-2882: Cryo-Molecular electron tomography of NTS-DBL1alphaCIDRgamma (N-t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2882 | |||||||||
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Title | Cryo-Molecular electron tomography of NTS-DBL1alphaCIDRgamma (N-terminal domain of PfEMP1-IT4Var60) | |||||||||
Map data | reconstruction of NTS-DBL1alphaCIDR1gamma Str1 | |||||||||
Sample |
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Keywords | Malaria / Rosetting / PfEMP1 | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | electron tomography / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Akhouri RR / Goel S / Furusho H / Skoglund U / Wahlgren M | |||||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Architecture of Human IgM in Complex with P. falciparum Erythrocyte Membrane Protein 1. Authors: Reetesh Raj Akhouri / Suchi Goel / Hirotoshi Furusho / Ulf Skoglund / Mats Wahlgren / Abstract: Plasmodium falciparum virulence is associated with sequestration of infected erythrocytes. Microvascular binding mediated by PfEMP1 in complex with non-immune immunoglobulin M (IgM) is common among ...Plasmodium falciparum virulence is associated with sequestration of infected erythrocytes. Microvascular binding mediated by PfEMP1 in complex with non-immune immunoglobulin M (IgM) is common among parasites that cause both severe childhood malaria and pregnancy-associated malaria. Here, we present cryo-molecular electron tomography structures of human IgM, PfEMP1 and their complex. Three-dimensional reconstructions of IgM reveal that it has a dome-like core, randomly oriented Fab2s units, and the overall shape of a turtle. PfEMP1 is a C- shaped molecule with a flexible N terminus followed by an arc-shaped backbone and a bulky C terminus that interacts with IgM. Our data demonstrate that the PfEMP1 binding pockets on IgM overlap with those of C1q, and the bulkiness of PfEMP1 limits the capacity of IgM to interact with PfEMP1. We suggest that P. falciparum exploits IgM to cluster PfEMP1 into an organized matrix to augment its affinity to host cell receptors. | |||||||||
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_2882.map.gz | 54.7 KB | EMDB map data format | |
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Header (meta data) | emd-2882-v30.xml emd-2882.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_2882.tif | 43.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2882 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2882 | HTTPS FTP |
-Validation report
Summary document | emd_2882_validation.pdf.gz | 154.9 KB | Display | EMDB validaton report |
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Full document | emd_2882_full_validation.pdf.gz | 154.1 KB | Display | |
Data in XML | emd_2882_validation.xml.gz | 4.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2882 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2882 | HTTPS FTP |
-Related structure data
Related structure data | 2883C 2884C 2885C 2886C 2887C 2888C 2889C 2890C 2891C 2892C 2893C 2894C 2895C 6554C C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2882.map.gz / Format: CCP4 / Size: 61.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of NTS-DBL1alphaCIDR1gamma Str1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.534 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 : NTS-DBL1alphaCIDR1gamma domain of PfEMP1-IT4Var60
Entire | Name: NTS-DBL1alphaCIDR1gamma domain of PfEMP1-IT4Var60 |
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Components |
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-Supramolecule #1000: NTS-DBL1alphaCIDR1gamma domain of PfEMP1-IT4Var60
Supramolecule | Name: NTS-DBL1alphaCIDR1gamma domain of PfEMP1-IT4Var60 / type: sample / ID: 1000 / Details: the sample was monodisperse. / Oligomeric state: Monomer / Number unique components: 1 |
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Molecular weight | Experimental: 87.4 KDa / Theoretical: 87 KDa |
-Macromolecule #1: NTS-DBL1alphaCIDR1gamma
Macromolecule | Name: NTS-DBL1alphaCIDR1gamma / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) Strain: FCR3S1.2 / synonym: Malaria Parasite / Location in cell: Infected erythrocyte membrane |
Molecular weight | Experimental: 87.4 KDa / Theoretical: 87 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: SHuffle T7 / Recombinant plasmid: pJ414 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.5 / Details: 20mM Hepes, 200mM NaCl |
Grid | Details: C-Flat (Copper grid with thin Carbon support) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 78 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78 K / Max: 100 K |
Specialist optics | Energy filter - Name: FEI |
Date | May 9, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 281 / Average electron dose: 40 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0015 µm / Nominal defocus min: 0.0008 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder: LN2 cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 ° / Tilt series - Axis1 - Angle increment: 0.5 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | CTF correction and alignment using gold particles |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Software - Name: COMET / Number images used: 281 |
CTF correction | Details: each frame |