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- EMDB-1449: The molecular architecture of cadherins in native epidermal desmo... -

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Basic information

Entry
Database: EMDB / ID: EMD-1449
TitleThe molecular architecture of cadherins in native epidermal desmosomes.
Map dataImage used for the isosurface representation, after segmentation and mild filtering
Sample
  • Sample: Cadherin Organisation in Native Desmosomes
  • Organelle or cellular component: Desmosome
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsAl-Amoudi A / Diez DC / Betts MJ / Frangakis AS
CitationJournal: Nature / Year: 2007
Title: The molecular architecture of cadherins in native epidermal desmosomes.
Authors: Ashraf Al-Amoudi / Daniel Castaño Díez / Matthew J Betts / Achilleas S Frangakis /
Abstract: Desmosomes are cadherin-based adhesive intercellular junctions, which are present in tissues such as heart and skin. Despite considerable efforts, the molecular interfaces that mediate adhesion ...Desmosomes are cadherin-based adhesive intercellular junctions, which are present in tissues such as heart and skin. Despite considerable efforts, the molecular interfaces that mediate adhesion remain obscure. Here we apply cryo-electron tomography of vitreous sections from human epidermis to visualize the three-dimensional molecular architecture of desmosomal cadherins at close-to-native conditions. The three-dimensional reconstructions show a regular array of densities at approximately 70 A intervals along the midline, with a curved shape resembling the X-ray structure of C-cadherin, a representative 'classical' cadherin. Model-independent three-dimensional image processing of extracted sub-tomograms reveals the cadherin organization. After fitting the C-cadherin atomic structure into the averaged sub-tomograms, we see a periodic arrangement of a trans W-like and a cis V-like interaction corresponding to molecules from opposing membranes and the same cell membrane, respectively. The resulting model of cadherin organization explains existing two-dimensional data and yields insights into a possible mechanism of cadherin-based cell adhesion.
History
DepositionNov 1, 2007-
Header (metadata) releaseNov 2, 2007-
Map releaseNov 2, 2008-
UpdateSep 30, 2015-
Current statusSep 30, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.36
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1449.gif

Downloads & links

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Map

FileDownload / File: emd_1449.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImage used for the isosurface representation, after segmentation and mild filtering
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6 Å/pix.
x 66 pix.
= 396. Å		6 Å/pix.
x 66 pix.
= 396. Å		6 Å/pix.
x 66 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.284 / Movie #1: 0.36
Minimum - Maximum-0.344899 - 1.65244
Average (Standard dev.)0.0332188 (±0.131843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-33-33-33
Dimensions666666
Spacing666666
CellA=B=C: 396 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z666
M x/y/z666666
origin x/y/z0.0000.0000.000
length x/y/z396.000396.000396.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-33-33-33
NC/NR/NS666666
D min/max/mean-0.3451.6520.033

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Supplemental data

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Sample components

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Entire : Cadherin Organisation in Native Desmosomes

EntireName: Cadherin Organisation in Native Desmosomes
Components
  • Sample: Cadherin Organisation in Native Desmosomes
  • Organelle or cellular component: Desmosome

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Supramolecule #1000: Cadherin Organisation in Native Desmosomes

SupramoleculeName: Cadherin Organisation in Native Desmosomes / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Desmosome

SupramoleculeName: Desmosome / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Epidermis

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

GridDetails: 200 mesh quantifoil grid
VitrificationCryogen name: NITROGEN / Instrument: OTHER / Details: Vitrification instrument: Leica EMPact 2 / Method: High pressure freezing

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49669 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 3.8 µm / Nominal magnification: 22500
Specialist opticsEnergy filter - Name: Gatan 2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 64.0 ° / Tilt series - Axis1 - Max angle: 64 °
TemperatureAverage: 100 K
Image recordingAverage electron dose: 40 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF
DetailsAverage number of projections used in the 3D reconstructions: 417.

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Atomic model buiding 1

Initial modelPDB ID:

1l3w

DetailsProtocol: Rigid body. Semi-automated fitting
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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