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- EMDB-6554: Cryo-Molecular electron tomography of IgM -

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Basic information

Entry
Database: EMDB / ID: EMD-6554
TitleCryo-Molecular electron tomography of IgM
Map dataIgM extended
Sample
  • Sample: IgM extended
  • Protein or peptide: Immunoglobulin M
KeywordsMalaria / Rosetting / IgM
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 25.0 Å
AuthorsAkhouri RR / Goel S / Furusho H / Skoglund U / Wahlgren M
CitationJournal: 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
DepositionDec 3, 2015-
Header (metadata) releaseJan 20, 2016-
Map releaseJan 20, 2016-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0046
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0046
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6554.tif

Downloads & links

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Map

FileDownload / File: emd_6554.map.gz / Format: CCP4 / Size: 8.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIgM extended
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.27 Å/pix.
x 157 pix.
= 355.919 Å		2.27 Å/pix.
x 90 pix.
= 204.03 Å		2.27 Å/pix.
x 165 pix.
= 374.055 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0046 / Movie #1: 0.0046
Minimum - Maximum0.00027951 - 0.01227563
Average (Standard dev.)0.00259619 (±0.00129452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions90165157
Spacing90165157
CellA: 374.055 Å / B: 204.03 Å / C: 355.919 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2672.2672.267
M x/y/z16590157
origin x/y/z0.0000.0000.000
length x/y/z374.055204.030355.919
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS16590157
D min/max/mean0.0000.0120.003

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Supplemental data

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Sample components

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Entire : IgM extended

EntireName: IgM extended
Components
  • Sample: IgM extended
  • Protein or peptide: Immunoglobulin M

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Supramolecule #1000: IgM extended

SupramoleculeName: IgM extended / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightExperimental: 950 KDa / Theoretical: 950 KDa

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Macromolecule #1: Immunoglobulin M

MacromoleculeName: Immunoglobulin M / type: protein_or_peptide / ID: 1 / Name.synonym: IgM / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human
Molecular weightExperimental: 950 KDa / Theoretical: 950 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES, 200 mM NaCl
GridDetails: C-Flat (Copper grid with thin Carbon support)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 78 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78 K / Max: 100 K
Specialist opticsEnergy filter - Name: FEI
DateJun 13, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 281 / Average electron dose: 40 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 37000
Sample stageSpecimen 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

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Image processing

DetailsCTF correction and alignment using gold particles
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Software - Name: COMET / Number images used: 281
CTF correctionDetails: each frame

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