[English] 日本語
Yorodumi
- EMDB-1703: Intracellular part of the desmosome -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

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

EMD-1703.png

Downloads & links

-
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
Voxel sizeX=Y=Z: 6 Å
Density
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

-
Supplemental data

-
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)

-
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)

-
Sample components

-
Entire : native skin tissue

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

-
Supramolecule #1000: native skin tissue

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging

-
Sample preparation

VitrificationCryogen name: NITROGEN / Instrument: OTHER

-
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

-
Image processing

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

+
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