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- EMDB-4608: Human Adenovirus type 3 fiber knob in complex with one copy of De... -

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Basic information

Entry
Database: EMDB / ID: EMD-4608
TitleHuman Adenovirus type 3 fiber knob in complex with one copy of Desmoglein-2
Map dataHuman Adenovirus type 3 fiber knob in complex with one DSG-2
Sample
  • Complex: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
    • Complex: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
      • Protein or peptide: Fiber protein
    • Complex: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
      • Protein or peptide: Desmoglein-2
Keywordsvirus receptor / adenovirus / vector / 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 / negative regulation of endothelial cell differentiation / Keratinization / 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 / negative regulation of endothelial cell differentiation / Keratinization / 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 / homophilic cell-cell adhesion / positive regulation of stem cell population maintenance / regulation of heart rate by cardiac conduction / intercalated disc / RHOG GTPase cycle / lateral plasma membrane / RAC2 GTPase cycle / maternal process involved in female pregnancy / RAC3 GTPase cycle / cell adhesion molecule binding / positive regulation of cell adhesion / response to progesterone / stem cell proliferation / cell-cell adhesion / cell-cell junction / cell junction / viral capsid / cell adhesion / apical plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / symbiont entry into host cell / negative regulation of apoptotic process / host cell nucleus / cell surface / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Desmosomal cadherin / : / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / 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, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / 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
Similarity search - Component
Biological speciesHuman adenovirus B serotype 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsEffantin G
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0001 France
CitationJournal: Nat Commun / Year: 2019
Title: CryoEM structure of adenovirus type 3 fibre with desmoglein 2 shows an unusual mode of receptor engagement.
Authors: Emilie Vassal-Stermann / Gregory Effantin / Chloe Zubieta / Wim Burmeister / Frédéric Iseni / Hongjie Wang / André Lieber / Guy Schoehn / Pascal Fender /
Abstract: Attachment of human adenovirus (HAd) to the host cell is a critical step of infection. Initial attachment occurs via the adenoviral fibre knob protein and a cellular receptor. Here we report the cryo- ...Attachment of human adenovirus (HAd) to the host cell is a critical step of infection. Initial attachment occurs via the adenoviral fibre knob protein and a cellular receptor. Here we report the cryo-electron microscopy (cryo-EM) structure of a <100 kDa non-symmetrical complex comprising the trimeric HAd type 3 fibre knob (HAd3K) and human desmoglein 2 (DSG2). The structure reveals a unique stoichiometry of 1:1 and 2:1 (DSG2: knob trimer) not previously observed for other HAd-receptor complexes. We demonstrate that mutating Asp261 in the fibre knob is sufficient to totally abolish receptor binding. These data shed new light on adenovirus infection strategies and provide insights for adenoviral vector development and structure-based design.
History
DepositionFeb 12, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qnt
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4608.png

Downloads & links

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Map

FileDownload / File: emd_4608.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Adenovirus type 3 fiber knob in complex with one DSG-2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 213.4 Å		1.07 Å/pix.
x 200 pix.
= 213.4 Å		1.07 Å/pix.
x 200 pix.
= 213.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.19289026 - 0.33513376
Average (Standard dev.)-0.000031167077 (±0.009299881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 213.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z213.400213.400213.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1930.335-0.000

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Supplemental data

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Sample components

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Entire : Human Adenovirus type 3 fibre knob in complex with one copy of De...

EntireName: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
Components
  • Complex: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
    • Complex: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
      • Protein or peptide: Fiber protein
    • Complex: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
      • Protein or peptide: Desmoglein-2

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Supramolecule #1: Human Adenovirus type 3 fibre knob in complex with one copy of De...

SupramoleculeName: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 96 KDa

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Supramolecule #2: Human Adenovirus type 3 fibre knob in complex with one copy of De...

SupramoleculeName: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human adenovirus B serotype 3

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Supramolecule #3: Human Adenovirus type 3 fibre knob in complex with one copy of De...

SupramoleculeName: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fiber protein

MacromoleculeName: Fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus B serotype 3
Molecular weightTheoretical: 20.95467 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NNTLWTGPKP EANCIIEYGK QNPDSKLTLI LVKNGGIVNG YVTLMGASDY VNTLFKNKNV SINVELYFDA TGHILPDSSS LKTDLELKY KQTADFSARG FMPSTTAYPF VLPNGTHNEN YIFGQCYYKA SDGALFPLEV TVMLNKRLPD SRTSYVMTFL W SLNAGLAP ETTQATLITS PFTFSYIRED

UniProtKB: Fiber protein

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Macromolecule #2: Desmoglein-2

MacromoleculeName: Desmoglein-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.268219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PVFTQDVFVG SVEELSAAHT LVMKINATDA EPNTLSKISY RIVSLEPAYP PVFYLNKDTG EIYTTSVTLD REEHSSYTLT VEARDGVKQ AQVQIRILDV NDNIPVVELE GMVEENQVNV EVTRIKVFDA DEIGSDNWLA NFTFASGNEG GYFHIETDAQ T NEGIVTLI ...String:
PVFTQDVFVG SVEELSAAHT LVMKINATDA EPNTLSKISY RIVSLEPAYP PVFYLNKDTG EIYTTSVTLD REEHSSYTLT VEARDGVKQ AQVQIRILDV NDNIPVVELE GMVEENQVNV EVTRIKVFDA DEIGSDNWLA NFTFASGNEG GYFHIETDAQ T NEGIVTLI KEVYMKNLDF SVIVANKAAF HKSIRSKYKP TPIPIKVKVK

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

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: 35.0 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: PDB ENTRY
PDB model - PDB ID:

1h7z

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139958
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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