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- EMDB-11678: Cadherin fit into cryo-ET map -

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Basic information

Entry
Database: EMDB / ID: EMD-11678
TitleCadherin fit into cryo-ET map
Map data
Sample
  • Organelle or cellular component: Desmosome from mouse liver
    • Protein or peptide: Desmoglein-2
    • Protein or peptide: Desmocollin-2
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-cell junction / 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
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) / Human (human)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsSikora M / Ermel UH / Seybold A / Kunz M / Calloni G / Reitz J / Vabulas RM / Hummer G / Frangakis AS
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, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateDec 23, 2020-
Current statusDec 23, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7a7d
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7a7d
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11678.png

Downloads & links

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Map

FileDownload / File: emd_11678.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 128 pix.
= 550.4 Å		4.3 Å/pix.
x 128 pix.
= 550.4 Å		4.3 Å/pix.
x 128 pix.
= 550.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0133 / Movie #1: 0.0133
Minimum - Maximum-0.06700626 - 0.21042718
Average (Standard dev.)7.7728895e-05 (±0.0054011894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-53-58-15
Dimensions128128128
Spacing128128128
CellA=B=C: 550.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z550.400550.400550.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-58-53-15
NC/NR/NS128128128
D min/max/mean-0.0670.2100.000

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Supplemental data

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Sample components

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Entire : Desmosome from mouse liver

EntireName: Desmosome from mouse liver
Components
  • Organelle or cellular component: Desmosome from mouse liver
    • Protein or peptide: Desmoglein-2
    • Protein or peptide: Desmocollin-2

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Supramolecule #1: Desmosome from mouse liver

SupramoleculeName: Desmosome from mouse liver / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Desmoglein-2

MacromoleculeName: Desmoglein-2 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 61.893297 KDa
SequenceString: AWITAPVALR EGEDLSKKNP IAKIHSDLAE ERGLKITYKY TGKGITEPPF GIFVFNKDTG ELNVTSILDR EETPFFLLTG YALDARGNN VEKPLELRIK VLDINDNEPV FTQDVFVGSV EELSAAHTLV MKINATDADE PNTLNSKISY RIVSLEPAYP P VFYLNKDT ...String:
AWITAPVALR EGEDLSKKNP IAKIHSDLAE ERGLKITYKY TGKGITEPPF GIFVFNKDTG ELNVTSILDR EETPFFLLTG YALDARGNN VEKPLELRIK VLDINDNEPV FTQDVFVGSV EELSAAHTLV MKINATDADE PNTLNSKISY RIVSLEPAYP P VFYLNKDT GEIYTTSVTL DREEHSSYTL TVEARDGNGE VTDKPVKQAQ VQIRILDVND NIPVVENKVL EGMVEENQVN VE VTRIKVF DADEIGSDNW LANFTFASGN EGGYFHIETD AQTNEGIVTL IKEVDYEEMK NLDFSVIVAN KAAFHKSIRS KYK PTPIPI KVKVKNVKEG IHFKSSVISI YVSESMDRSS KGQIIGNFQA FDEDTGLPAH ARYVKLEDRD NWISVDSVTS EIKL AKLPD FESRYVQNGT YTVKIVAISE DYPRKTITGT VLINVEDIND NCPTLIEPVQ TICHDAEYVN VTAEDLDGHP NSGPF SFSV IDKPPGMAEK WKIARQESTS VLLQQSEKKL GRSEIQFLIS DNQGFSCPEK QVLTLTVCEC LHGSGCREAH

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Macromolecule #2: Desmocollin-2

MacromoleculeName: Desmocollin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 60.86984 KDa
SequenceString: RWAPIPCSML ENSLGPFPLF LQQVQSDTAQ NYTIYYSIRG PGVDQEPRNL FYVERDTGNL YCTRPVDREQ YESFEIIAFA TTPDGYTPE LPLPLIIKIE DENDNYPIFT EETYTFTIFE NCRVGTTVGQ VCATDKDEPD TMHTRLKYSI IGQVPPSPTL F SMHPTTGV ...String:
RWAPIPCSML ENSLGPFPLF LQQVQSDTAQ NYTIYYSIRG PGVDQEPRNL FYVERDTGNL YCTRPVDREQ YESFEIIAFA TTPDGYTPE LPLPLIIKIE DENDNYPIFT EETYTFTIFE NCRVGTTVGQ VCATDKDEPD TMHTRLKYSI IGQVPPSPTL F SMHPTTGV ITTTSSQLDR ELIDKYQLKI KVQDMDGQYF GLQTTSTCII NIDDVNDHLP TFTRTSYVTS VEENTVDVEI LR VTVEDKD LVNTANWRAN YTILKGNENG NFKIVTDAKT NEGVLCVVKP LNYEEKQQMI LQIGVVNEAP FSREASPRSA MST ATVTVN VEDQDEGPEC NPPIQTVRMK ENAEVGTTSN GYKAYDPETR SSSGIRYKKL TDPTGWVTID ENTGSIKVFR SLDR EAETI KNGIYNITVL ASDQGGRTCT GTLGIILQDV NDNSPFIPKK TVIICKPTMS SAEIVAVDPD EPIHGPPFDF SLESS TSEV QRMWRLKAIN DTAARLSYQN DPPFGSYVVP ITVRDRLGMS SVTSLDVTLC DCITENDCTH

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum SE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 2.0 sec. / Average electron dose: 1.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 3656
ExtractionNumber tomograms: 12 / Number images used: 9000
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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