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- EMDB-2889: Cryo-Molecular electron tomography of human non-immune soluble pe... -

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Basic information

Entry
Database: EMDB / ID: EMD-2889
TitleCryo-Molecular electron tomography of human non-immune soluble pentameric IgM
Map dataReconstruction of human pentameric IgM str4
Sample
  • Sample: Human non-immune pentameric IgM
  • Protein or peptide: Immunoglobulin M
KeywordsMalaria / Rosetting / IgM
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 20.0 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
DepositionFeb 8, 2015-
Header (metadata) releaseFeb 25, 2015-
Map releaseJan 13, 2016-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / 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_2889.tif

Downloads & links

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Map

FileDownload / File: emd_2889.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of human pentameric IgM str4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.27 Å/pix.
x 128 pix.
= 290.176 Å		2.27 Å/pix.
x 128 pix.
= 290.176 Å		2.27 Å/pix.
x 128 pix.
= 290.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0042 / Movie #1: 0.0046
Minimum - Maximum0.00109054 - 0.00834144
Average (Standard dev.)0.00295507 (±0.00085307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 290.176 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2672.2672.267
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z290.176290.176290.176
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean0.0010.0080.003

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Supplemental data

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Sample components

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Entire : Human non-immune pentameric IgM

EntireName: Human non-immune pentameric IgM
Components
  • Sample: Human non-immune pentameric IgM
  • Protein or peptide: Immunoglobulin M

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Supramolecule #1000: Human non-immune pentameric IgM

SupramoleculeName: Human non-immune pentameric IgM / type: sample / ID: 1000
Details: the sample was polydisperse using Dynamic Light Scattering.
Oligomeric state: Monomer / Number unique components: 1
Molecular weightExperimental: 949 KDa / Theoretical: 1.0 MDa

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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 / Location in cell: Soluble in serum
Molecular weightExperimental: 949 KDa / Theoretical: 1.0 MDa

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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 mg/mL
BufferpH: 7.5 / Details: 20mM Tris, 200mM 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
DateDec 6, 2013
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: 0.0015 µm / Nominal defocus min: 0.0007 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 on each tilt
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Software - Name: COMET / Number images used: 281
CTF correctionDetails: each frame

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