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- EMDB-11778: HAd7 knob in complex with 3 EC2-EC3 modules of DSG-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-11778
TitleHAd7 knob in complex with 3 EC2-EC3 modules of DSG-2
Map data
SampleHuman adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2:
(Desmoglein-2) x 2 / (Fiber) x 2
Function / homology
Function and homology information


Purkinje myocyte development / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / desmosome organization / cornified envelope / desmosome / regulation of ventricular cardiac muscle cell action potential / adhesion receptor-mediated virion attachment to host cell / cornification / regulation of heart rate by cardiac conduction ...Purkinje myocyte development / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / desmosome organization / cornified envelope / desmosome / regulation of ventricular cardiac muscle cell action potential / adhesion receptor-mediated virion attachment to host cell / cornification / regulation of heart rate by cardiac conduction / keratinization / intercalated disc / maternal process involved in female pregnancy / lateral plasma membrane / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / cell-cell adhesion / response to progesterone / viral capsid / cell junction / cell-cell junction / apical plasma membrane / viral entry into host cell / cell adhesion / intracellular membrane-bounded organelle / calcium ion binding / host cell nucleus / cell surface / extracellular exosome / integral component of membrane / plasma membrane / nucleus
Adenovirus fibre protein / Desmosomal cadherin / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Cadherin-like / Adenovirus pIV-like, attachment domain / Attachment protein shaft domain superfamily / Desmoglein / Cadherin-like superfamily / Cadherin conserved site / Catenin binding domain superfamily
Desmoglein-2 / Fiber
Biological speciesHomo sapiens (human) / Human adenovirus B serotype 7
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsEffantin G / Vassal-Stermann E / Fender P
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.
Validation ReportPDB-ID: 7agf

SummaryFull reportAbout validation report
History
DepositionSep 22, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing 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-7agf
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11778.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.012199558 - 0.023372756
Average (Standard dev.)0.0000086076 (±0.00085888605)
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-0.0120.0230.000

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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
Number of components: 5

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Component #1: protein, Human adenovirus type 7 knob in complex with 2 EC2 EC3 m...

ProteinName: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2
Recombinant expression: No
MassExperimental: 130 kDa

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Component #2: protein, Desmoglein-2

ProteinName: Desmoglein-2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Fiber

ProteinName: Fiber / Recombinant expression: No
SourceSpecies: Human adenovirus B serotype 7
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Fiber

ProteinName: Fiber / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.489217 kDa
SourceSpecies: Human adenovirus B serotype 7
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Desmoglein-2

ProteinName: Desmoglein-2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 27.126275 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/mL / pH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 58219
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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