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- EMDB-1703: Intracellular part of the desmosome -

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Basic information

Entry
Database: EMDB / ID: EMD-1703
TitleIntracellular part of the desmosome
Map datasub-Tomogram Average
Sample
  • Sample: native skin tissue
  • Organelle or cellular component: desmosome
Keywordsdesmosome / cryo-electron tomography / vitreous sections
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsAl-Amoudi A / Frangakis AS
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: The three-dimensional molecular structure of the desmosomal plaque.
Authors: Ashraf Al-Amoudi / Daniel Castaño-Diez / Damien P Devos / Robert B Russell / Graham T Johnson / Achilleas S Frangakis /
Abstract: The cytoplasmic surface of intercellular junctions is a complex network of molecular interactions that link the extracellular region of the desmosomal cadherins with the cytoskeletal intermediate ...The cytoplasmic surface of intercellular junctions is a complex network of molecular interactions that link the extracellular region of the desmosomal cadherins with the cytoskeletal intermediate filaments. Although 3D structures of the major plaque components are known, the overall architecture remains unknown. We used cryoelectron tomography of vitreous sections from human epidermis to record 3D images of desmosomes in vivo and in situ at molecular resolution. Our results show that the architecture of the cytoplasmic surface of the desmosome is a 2D interconnected quasiperiodic lattice, with a similar spatial organization to the extracellular side. Subtomogram averaging of the plaque region reveals two distinct layers of the desmosomal plaque: a low-density layer closer to the membrane and a high-density layer further away from the membrane. When combined with a heuristic, allowing simultaneous constrained fitting of the high-resolution structures of the major plaque proteins (desmoplakin, plakophilin, and plakoglobin), it reveals their mutual molecular interactions and explains their stoichiometry. The arrangement suggests that alternate plakoglobin-desmoplakin complexes create a template on which desmosomal cadherins cluster before they stabilize extracellularly by binding at their N-terminal tips. Plakophilins are added as a molecular reinforcement to fill the gap between the formed plaque complexes and the plasma membrane.
History
DepositionFeb 11, 2010-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1703.png

Downloads & links

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Map

FileDownload / File: emd_1703.map.gz / Format: CCP4 / Size: 526.4 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsub-Tomogram Average
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6 Å/pix.
x 46 pix.
= 276. Å		6 Å/pix.
x 65 pix.
= 390. Å		6 Å/pix.
x 46 pix.
= 276. 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: 6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.09588459 - 0.06440032
Average (Standard dev.)-0.00072517 (±0.01461217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions654646
Spacing654646
CellA: 276.0 Å / B: 390.0 Å / C: 276.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z666
M x/y/z466546
origin x/y/z0.0000.0000.000
length x/y/z276.000390.000276.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS466546
D min/max/mean-0.0960.064-0.001

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Supplemental data

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Segmentation: Masked sub-tomogram average for residual noise removal

AnnotationMasked sub-tomogram average for residual noise removal
Fileemd_1703_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: symmetrized sub-tomogram average

Annotationsymmetrized sub-tomogram average
Fileemd_1703_msk_2.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 : native skin tissue

EntireName: native skin tissue
Components
  • Sample: native skin tissue
  • Organelle or cellular component: desmosome

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Supramolecule #1000: native skin tissue

SupramoleculeName: native skin tissue / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: desmosome

SupramoleculeName: desmosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: desmosome / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: HOME BUILD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF

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