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- EMDB-1052: Untangling desmosomal knots with electron tomography. -

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Basic information

Entry
Database: EMDB / ID: EMD-1052
TitleUntangling desmosomal knots with electron tomography.
Map dataThis is a 3D reconstruction map of an desmosome based on high pressure freezing/freeze-subsitution electron tomography
Sample
  • Sample: mouse skin
  • Organelle or cellular component: desmosome
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM / negative staining / Resolution: 30.0 Å
AuthorsHe W / Cowin P / Stokes DL
CitationJournal: Science / Year: 2003
Title: Untangling desmosomal knots with electron tomography.
Authors: Wanzhong He / Pamela Cowin / David L Stokes /
Abstract: Cell adhesion by adherens junctions and desmosomes relies on interactions between cadherin molecules. However, the molecular interfaces that define molecular specificity and that mediate adhesion ...Cell adhesion by adherens junctions and desmosomes relies on interactions between cadherin molecules. However, the molecular interfaces that define molecular specificity and that mediate adhesion remain controversial. We used electron tomography of plastic sections from neonatal mouse skin to visualize the organization of desmosomes in situ. The resulting three-dimensional maps reveal individual cadherin molecules forming discrete groups and interacting through their tips. Fitting of an x-ray crystal structure for C-cadherin to these maps is consistent with a flexible intermolecular interface mediated by an exchange of amino-terminal tryptophans. This flexibility suggests a novel mechanism for generating both cis and trans interactions and for propagating these adhesive interactions along the junction.
History
DepositionAug 28, 2003-
Header (metadata) releaseAug 28, 2003-
Map releaseSep 28, 2003-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

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  • Solid view (volume rendering)
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1q55
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1q5a
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1q5b
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1q5c
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  • Simplified surface model
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1052.gif

Downloads & links

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Map

FileDownload / File: emd_1052.map.gz / Format: CCP4 / Size: 41.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThis is a 3D reconstruction map of an desmosome based on high pressure freezing/freeze-subsitution electron tomography
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.27 Å/pix.
x 85 pix.
= 617.61 Å		7.27 Å/pix.
x 512 pix.
= 3720.192 Å		7.27 Å/pix.
x 512 pix.
= 3720.192 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: 7.266 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1760.0
Minimum - Maximum-1866.0 - 2603.0
Average (Standard dev.)1323.980000000000018 (±218.754999999999995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions51251285
Spacing51251285
CellA: 3720.19 Å / B: 3720.19 Å / C: 617.61 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.2667.2667.266
M x/y/z51251285
origin x/y/z0.0000.0000.000
length x/y/z3720.1923720.192617.610
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS51251285
D min/max/mean-1866.0002603.0001323.977

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Supplemental data

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Sample components

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Entire : mouse skin

EntireName: mouse skin
Components
  • Sample: mouse skin
  • Organelle or cellular component: desmosome

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Supramolecule #1000: mouse skin

SupramoleculeName: mouse skin / type: sample / ID: 1000
Details: Skin from newborn mice frozen by high-pressure freezer followed by freeze-substitution, embedding in Epon resin and thin sectioning
Oligomeric state: desmosome / Number unique components: 1

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Supramolecule #1: desmosome

SupramoleculeName: desmosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: desmosome
Details: in-situ desmosome from frozen skin; fresh skin from newborn mice frozen immediately with high pressure freezer.
Number of copies: 1 / Oligomeric state: unique / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Mus musculus (house mouse) / synonym: mouse / Tissue: mouse / Cell: skin / Organelle: cell junction / Location in cell: between two cells plasma membrane

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography

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Sample preparation

BufferpH: 7.4 / Details: 0.5mM MgCl2 and 1-2mM CaCl2 in PBS
StainingType: NEGATIVE
Details: staining en bloc freeze-substitution with 1% OsO4/0.1% uranyl acetate in acetone, thin section stained with 3% uranyl acetate/SATO Pb post-stain
GridDetails: 200 mesh thin bar hexgonal cooper grid with formvar
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: OTHER
Details: Vitrification instrument: BalTec HPM 010. high pressure freezing at 2050 bar with liquid nitrigen
Timed resolved state: 50msec / Method: High pressure freezing

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureMin: 293 K / Max: 293 K / Average: 293 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected with thin carbon at 200-390kx
Legacy - Electron beam tilt params: 0
Detailsdose corresponds to the cumulative dose for the entire the dataset.
DateNov 23, 2002
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Number real images: 300 / Details: imaging directly on the CCD
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: high tilt / Specimen holder model: OTHER / Tilt series - Axis1 - Angle increment: 1 °

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Image processing

Detailsdetails 50nm thin section stained with 3% uranyl acetate and followed by SATO Lead stain, picked on formvar coated grids and both sides coated 5-10nm amorphous carbon.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: IMOD
Details: tomographic reconstruction from dual axis tilt series (tilt range:-78/+73; -68/+75,interval:1 degree).
Number images used: 150
CTF correctionDetails: no CTF correction

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Atomic model buiding 1

Initial modelPDB ID:

1l3w

SoftwareName: AmiraMol 3.0
DetailsProtocol: Rigid Body. tomographic map used for fitting C-cadherin structure. #Results deposited in PDB database under codes 1Q55, 1Q5A, 1Q5B and 1Q5C.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-1q55:
W-shaped trans interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography

PDB-1q5a:
S-shaped trans interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography

PDB-1q5b:
lambda-shaped TRANS and CIS interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography

PDB-1q5c:
S-S-lambda-shaped TRANS and CIS interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography

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