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- EMDB-11779: HAd7 knob in complex with 2 EC2-EC3 modules of DSG-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-11779
TitleHAd7 knob in complex with 2 EC2-EC3 modules of DSG-2
Map dataHAd7 knob in complex with 2 DSG-2 modules
Sample
  • Complex: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2
    • Complex: Desmoglein-2
      • Protein or peptide: Desmoglein-2
    • Complex: Fiber
      • Protein or peptide: Fiber
Keywordsadenovirus / cell receptor / complex / VIRAL PROTEIN
Function / homology
Function and homology information


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 ...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 / adhesion receptor-mediated virion attachment to host cell / 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 / stem cell proliferation / cell-cell adhesion / cell junction / viral capsid / cell-cell junction / cell adhesion / apical plasma membrane / symbiont entry into host cell / intracellular membrane-bounded organelle / calcium ion binding / negative regulation of apoptotic process / host cell nucleus / cell surface / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Desmosomal cadherin / : / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Catenin binding domain superfamily / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain ...Desmosomal cadherin / : / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Catenin binding domain superfamily / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Fiber protein / Desmoglein-2 / Fiber
Similarity search - Component
Biological speciesHomo sapiens (human) / Human adenovirus B serotype 7
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsEffantin G / Vassal-Stermann E
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0001 France
CitationJournal: Viruses / Year: 2020
Title: Binding Mechanism Elucidation of the Acute Respiratory Disease Causing Agent Adenovirus of Serotype 7 to Desmoglein-2.
Authors: Marc-André Hograindleur / Gregory Effantin / Daphna Fenel / Caroline Mas / André Lieber / Guy Schoehn / Pascal Fender / Emilie Vassal-Stermann /
Abstract: The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human ...The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human adenoviruses, adenovirus of serotype 7 (HAdV7) is one of the most virulent serotypes. This virus regularly re-emerges in Asia and has just been the cause of several deaths in the United States. A critical step of the virus life cycle is the attachment of the knob domain of the fiber (HAd7K) to the cellular receptor desmoglein-2 (DSG2). Complexes between the fiber knob and two extracellular domains of DSG2 have been produced. Their characterization by biochemical and biophysical methods show that these two domains are sufficient for the interaction and that the trimeric HAd7K could accommodate up to three DSG2 receptor molecules. The cryo-electron microscopy (cryo-EM) structure of these complexes at 3.1 Å resolution confirmed the biochemical data, and allowed the identification of the critical amino acid residues for this interaction, which shows similarities with other DSG2 interacting adenoviruses, despite a low homology in the primary sequences.
History
DepositionSep 22, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7agg
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11779.png

Downloads & links

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Map

FileDownload / File: emd_11779.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHAd7 knob in complex with 2 DSG-2 modules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 318 pix.
= 206.7 Å		0.65 Å/pix.
x 318 pix.
= 206.7 Å		0.65 Å/pix.
x 318 pix.
= 206.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.014132425 - 0.022662485
Average (Standard dev.)0.0000049820937 (±0.00079149817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions318318318
Spacing318318318
CellA=B=C: 206.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z318318318
origin x/y/z0.0000.0000.000
length x/y/z206.700206.700206.700
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS318318318
D min/max/mean-0.0140.0230.000

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Supplemental data

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Sample components

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Entire : Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of...

EntireName: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2
Components
  • Complex: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2
    • Complex: Desmoglein-2
      • Protein or peptide: Desmoglein-2
    • Complex: Fiber
      • Protein or peptide: Fiber

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Supramolecule #1: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of...

SupramoleculeName: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 110 KDa

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Supramolecule #2: Desmoglein-2

SupramoleculeName: Desmoglein-2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Fiber

SupramoleculeName: Fiber / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human adenovirus B serotype 7

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Macromolecule #1: Fiber

MacromoleculeName: Fiber / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus B serotype 7
Molecular weightTheoretical: 23.489217 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMGLTFNS NNICIDDNIN TLWTGVNPTT ANCQIMASSE SNDCKLILTL VKTGALVTAF VYVIGVSNDF NMLTTHKNIN FTAELFFDS TGNLLTSLSS LKTPLNHKSG QNMATGALTN AKGFMPSTTA YPFNVNSREK ENYIYGTCYY TASDHTAFPI D ISVMLNQR ...String:
GSHMGLTFNS NNICIDDNIN TLWTGVNPTT ANCQIMASSE SNDCKLILTL VKTGALVTAF VYVIGVSNDF NMLTTHKNIN FTAELFFDS TGNLLTSLSS LKTPLNHKSG QNMATGALTN AKGFMPSTTA YPFNVNSREK ENYIYGTCYY TASDHTAFPI D ISVMLNQR ALNNETSYCI RVTWSWNTGV APEVQTSATT LVTSPFTFYY IREDD

UniProtKB: Fiber

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Macromolecule #2: Desmoglein-2

MacromoleculeName: Desmoglein-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.126275 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QGAMEVLDIN DNEPVFTQDV FVGSVEELSA AHTLVMKINA TDADEPNTLN SKISYRIVSL EPAYPPVFYL NKDTGEIYTT SVTLDREEH SSYTLTVEAR DGNGEVTDKP VKQAQVQIRI LDVNDNIPVV ENKVLEGMVE ENQVNVEVTR IKVFDADEIG S DNWLANFT ...String:
QGAMEVLDIN DNEPVFTQDV FVGSVEELSA AHTLVMKINA TDADEPNTLN SKISYRIVSL EPAYPPVFYL NKDTGEIYTT SVTLDREEH SSYTLTVEAR DGNGEVTDKP VKQAQVQIRI LDVNDNIPVV ENKVLEGMVE ENQVNVEVTR IKVFDADEIG S DNWLANFT FASGNEGGYF HIETDAQTNE GIVTLIKEVD YEEMKNLDFS VIVANKAAFH KSIRSKYKPT PIPIKVKVKN VK EGI

UniProtKB: Desmoglein-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97190
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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