[English] 日本語
Yorodumi
- EMDB-1374: The molecular architecture of cadherins in native epidermal desmo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1374
TitleThe molecular architecture of cadherins in native epidermal desmosomes.
Map dataThis is the average of the subtomograms.
Sample
  • Sample: architecture of cadherin molecules
  • Organelle or cellular component: cadherin
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsAl-Amoudi A / Castano Diez D / 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
DepositionJun 16, 2007-
Header (metadata) releaseJun 16, 2007-
Map releaseJun 16, 2009-
UpdateSep 30, 2015-
Current statusSep 30, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1374.png

Downloads & links

-
Map

FileDownload / File: emd_1374.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the average of the subtomograms.
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: 0.009 / Movie #1: 0.01
Minimum - Maximum-1.26741 - 1.18232
Average (Standard dev.)-0.000000000004609 (±0.124566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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/NS000
NC/NR/NS666666
D min/max/mean-1.2671.182-0.000

-
Supplemental data

-
Sample components

-
Entire : architecture of cadherin molecules

EntireName: architecture of cadherin molecules
Components
  • Sample: architecture of cadherin molecules
  • Organelle or cellular component: cadherin

-
Supramolecule #1000: architecture of cadherin molecules

SupramoleculeName: architecture of cadherin molecules / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: cadherin

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging

-
Sample preparation

VitrificationCryogen name: NITROGEN / Instrument: OTHER / Details: Vitrification instrument: Leica EMPact 2 / Method: High pressure freezing

-
Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 100 K
Specialist opticsEnergy filter - Name: Gatan 2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV
DateJun 2, 2006
Image recordingAverage electron dose: 40 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus min: 3.8 µm / Nominal magnification: 22500
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: 64.0 ° / Tilt series - Axis1 - Max angle: 64 °
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF

-
Atomic model buiding 1

Initial modelPDB ID:

1l3w

DetailsProtocol: Rigid body. The fitting procedure is described in the supplementary material of the paper
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more