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- PDB-7a7d: Cadherin fit into cryo-ET map -

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Basic information

Entry
Database: PDB / ID: 7a7d
TitleCadherin fit into cryo-ET map
Components
  • Desmocollin-2
  • Desmoglein-2
KeywordsCELL ADHESION / Cadherin / Desmosome
Function / homology
Function and homology information


cardiac muscle cell-cardiac muscle cell adhesion / Purkinje myocyte development / positive regulation of protein localization to cell-cell junction / 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 / negative regulation of endothelial cell differentiation / negative regulation of inflammatory response to wounding / desmosome ...cardiac muscle cell-cardiac muscle cell adhesion / Purkinje myocyte development / positive regulation of protein localization to cell-cell junction / 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 / negative regulation of endothelial cell differentiation / negative regulation of inflammatory response to wounding / desmosome / mesenchymal to epithelial transition / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins / positive regulation of p38MAPK cascade / negative regulation of epithelial to mesenchymal transition / positive regulation of sprouting angiogenesis / positive regulation of stem cell population maintenance / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of heart rate by cardiac conduction / RHOG GTPase cycle / intercalated disc / RAC2 GTPase cycle / RAC3 GTPase cycle / lateral plasma membrane / maternal process involved in female pregnancy / cell adhesion molecule binding / positive regulation of cell adhesion / response to progesterone / cellular response to starvation / stem cell proliferation / adherens junction / cell-cell adhesion / cell junction / cell-cell junction / cytoplasmic vesicle / cell adhesion / apical plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / negative regulation of apoptotic process / cell surface / endoplasmic reticulum / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Desmosomal cadherin / : / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. ...Desmosomal cadherin / : / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Desmocollin-2 / Desmoglein-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 26 Å
AuthorsSikora, M. / Ermel, U.H. / Seybold, A. / Kunz, M. / Calloni, G. / Reitz, J. / Vabulas, R.M. / Hummer, G. / Frangakis, A.S.
CitationJournal: 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
DepositionAug 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
A: Desmoglein-2
B: Desmoglein-2
C: Desmoglein-2
D: Desmoglein-2
E: Desmoglein-2
F: Desmoglein-2
G: Desmoglein-2
a: Desmocollin-2
b: Desmocollin-2
c: Desmocollin-2
d: Desmocollin-2
e: Desmocollin-2
f: Desmocollin-2
g: Desmocollin-2


Theoretical massNumber of molelcules
Total (without water)859,34214
Polymers859,34214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11300 Å2
ΔGint-59 kcal/mol
Surface area450500 Å2
MethodPISA

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Components

#1: Protein
Desmoglein-2 / Cadherin family member 5 / HDGC


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
Desmocollin-2 / Cadherin family member 2 / Desmocollin-3 / Desmosomal glycoprotein II / Desmosomal glycoprotein III


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 interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Desmosome from mouse liver / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Quantum SE
Image scansMovie frames/image: 4

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 26 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3656 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 12 / Num. of volumes extracted: 9000

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