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- EMDB-1967: Cryo-electron tomography of the red blood cell cytoskeleton -

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Basic information

Entry
Database: EMDB / ID: EMD-1967
TitleCryo-electron tomography of the red blood cell cytoskeleton
Map dataCryo-electron tomogram of an isolated mouse red blood cell membrane skeleton after anisotropic diffusion
Sample
  • Sample: Mouse red blood cell cytoskeleton
  • Organelle or cellular component: Cytoskeleton
Keywordsspectrin network / erythrocyte / membrane skeleton
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsNans A / Mohandas N / Stokes DL
CitationJournal: Biophys J / Year: 2011
Title: Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography.
Authors: Andrea Nans / Narla Mohandas / David L Stokes /
Abstract: Erythrocytes possess a spectrin-based cytoskeleton that provides elasticity and mechanical stability necessary to survive the shear forces within the microvasculature. The architecture of this ...Erythrocytes possess a spectrin-based cytoskeleton that provides elasticity and mechanical stability necessary to survive the shear forces within the microvasculature. The architecture of this membrane skeleton and the nature of its intermolecular contacts determine the mechanical properties of the skeleton and confer the characteristic biconcave shape of red cells. We have used cryo-electron tomography to evaluate the three-dimensional topology in intact, unexpanded membrane skeletons from mouse erythrocytes frozen in physiological buffer. The tomograms reveal a complex network of spectrin filaments converging at actin-based nodes and a gradual decrease in both the density and the thickness of the network from the center to the edge of the cell. The average contour length of spectrin filaments connecting junctional complexes is 46 ± 15 nm, indicating that the spectrin heterotetramer in the native membrane skeleton is a fraction of its fully extended length (∼190 nm). Higher-order oligomers of spectrin were prevalent, with hexamers and octamers seen between virtually every junctional complex in the network. Based on comparisons with expanded skeletons, we propose that the oligomeric state of spectrin is in a dynamic equilibrium that facilitates remodeling of the network as the cell changes shape in response to shear stress.
History
DepositionSep 13, 2011-
Header (metadata) releaseOct 5, 2011-
Map releaseNov 17, 2011-
UpdateDec 9, 2011-
Current statusDec 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

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

EMD-1967-sam...

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Map

FileDownload / File: emd_1967.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryo-electron tomogram of an isolated mouse red blood cell membrane skeleton after anisotropic diffusion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.3 Å/pix.
x 150 pix.
= 1095. Å		7.3 Å/pix.
x 1655 pix.
= 12081.5 Å		7.3 Å/pix.
x 1655 pix.
= 12081.5 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: 7.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 18800.0
Minimum - Maximum0.0 - 32767.0
Average (Standard dev.)18931.318359379998583 (±2221.0151367200001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin1000
Dimensions16551655150
Spacing16551655150
CellA: 12081.5 Å / B: 12081.5 Å / C: 1095.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.37.37.3
M x/y/z16551655150
origin x/y/z0.0000.0000.000
length x/y/z12081.50012081.5001095.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS0100
NC/NR/NS16551655150
D min/max/mean0.00032767.00018931.318

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Supplemental data

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Supplemental map: emd 1967 additional 1.map

Fileemd_1967_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse red blood cell cytoskeleton

EntireName: Mouse red blood cell cytoskeleton
Components
  • Sample: Mouse red blood cell cytoskeleton
  • Organelle or cellular component: Cytoskeleton

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Supramolecule #1000: Mouse red blood cell cytoskeleton

SupramoleculeName: Mouse red blood cell cytoskeleton / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Cytoskeleton

SupramoleculeName: Cytoskeleton / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Membrane skeleton / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse / Cell: erythrocyte / Organelle: cytoskeleton

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: 2mM sodium phosphate
GridDetails: 200 mesh molybdenum
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 123 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: homemade / Method: Blot for 5 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 84 K
Specialist opticsEnergy filter - Name: omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateApr 20, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 70 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40859 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 9.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder: side-entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER / Tilt series - Axis1 - Min angle: -66 ° / Tilt series - Axis1 - Max angle: 66 ° / Tilt series - Axis1 - Angle increment: 2 °

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: Protomo / Number images used: 67

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