+Open data
-Basic information
Entry | Database: PDB / ID: 7a7d | ||||||
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Title | Cadherin fit into cryo-ET map | ||||||
Components |
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Keywords | CELL ADHESION / Cadherin / Desmosome | ||||||
Function / homology | Function and homology information cardiac muscle cell-cardiac muscle cell adhesion / Purkinje myocyte development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential ...cardiac muscle cell-cardiac muscle cell adhesion / Purkinje myocyte development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of heart rate by cardiac conduction / intercalated disc / RHOG GTPase cycle / lateral plasma membrane / RAC2 GTPase cycle / RAC3 GTPase cycle / maternal process involved in female pregnancy / cell adhesion molecule binding / cellular response to starvation / response to progesterone / adherens junction / cell-cell adhesion / cell junction / cell-cell junction / cytoplasmic vesicle / cell adhesion / apical plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / cell surface / endoplasmic reticulum / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 26 Å | ||||||
Authors | Sikora, M. / Ermel, U.H. / Seybold, A. / Kunz, M. / Calloni, G. / Reitz, J. / Vabulas, R.M. / Hummer, G. / Frangakis, A.S. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Authors: Mateusz Sikora / Utz H Ermel / Anna Seybold / Michael Kunz / Giulia Calloni / Julian Reitz / R Martin Vabulas / Gerhard Hummer / Achilleas S Frangakis / Abstract: Desmosomes are cell-cell junctions that link tissue cells experiencing intense mechanical stress. Although the structure of the desmosomal cadherins is known, the desmosome architecture-which is ...Desmosomes are cell-cell junctions that link tissue cells experiencing intense mechanical stress. Although the structure of the desmosomal cadherins is known, the desmosome architecture-which is essential for mediating numerous functions-remains elusive. Here, we recorded cryo-electron tomograms (cryo-ET) in which individual cadherins can be discerned; they appear variable in shape, spacing, and tilt with respect to the membrane. The resulting sub-tomogram average reaches a resolution of ∼26 Å, limited by the inherent flexibility of desmosomes. To address this challenge typical of dynamic biological assemblies, we combine sub-tomogram averaging with atomistic molecular dynamics (MD) simulations. We generate models of possible cadherin arrangements and perform an in silico screening according to biophysical and structural properties extracted from MD simulation trajectories. We find a truss-like arrangement of cadherins that resembles the characteristic footprint seen in the electron micrograph. The resulting model of the desmosomal architecture explains their unique biophysical properties and strength. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7a7d.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7a7d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a7d_validation.pdf.gz | 862 KB | Display | wwPDB validaton report |
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Full document | 7a7d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7a7d_validation.xml.gz | 195.4 KB | Display | |
Data in CIF | 7a7d_validation.cif.gz | 302 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/7a7d ftp://data.pdbj.org/pub/pdb/validation_reports/a7/7a7d | HTTPS FTP |
-Related structure data
Related structure data | 11678MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 61893.297 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14126 #2: Protein | Mass: 60869.840 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02487 Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: TISSUE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Desmosome from mouse liver / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 1.95 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum SE |
Image scans | Movie frames/image: 4 |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 26 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3656 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 12 / Num. of volumes extracted: 9000 |