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- EMDB-4609: Human Adenovirus type 3 fiber knob in complex with two copies of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4609
TitleHuman Adenovirus type 3 fiber knob in complex with two copies of Desmoglein-2
Map data
Sample
  • Complex: Human Adenovirus type 3 fibre knob in complex with two copies of Desmoglein 2
    • Complex: Human Adenovirus type 3 fibre knob in complex with two copies of Desmoglein 2
      • Protein or peptide: Fiber protein
    • Complex: Desmoglein 2
      • Protein or peptide: Desmoglein-2
Keywordsvirus receptor / adenovirus / vector / VIRAL PROTEIN
Function / homology
Function and homology information


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 / adhesion receptor-mediated virion attachment to host cell ...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 / adhesion receptor-mediated virion attachment to host cell / 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 / response to progesterone / cell-cell adhesion / cell-cell junction / cell junction / viral capsid / cell adhesion / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / host cell nucleus / cell surface / extracellular exosome / plasma membrane
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
Similarity search - Component
Biological speciesHuman adenovirus B serotype 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qnu
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4609.png

Downloads & links

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Map

FileDownload / File: emd_4609.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.16779897 - 0.25906238
Average (Standard dev.)-0.0000046397763 (±0.008194085)
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-0.1680.259-0.000

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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 two copies of ...

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

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Supramolecule #1: Human Adenovirus type 3 fibre knob in complex with two copies of ...

SupramoleculeName: Human Adenovirus type 3 fibre knob in complex with two copies of Desmoglein 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 116 KDa

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Supramolecule #2: Human Adenovirus type 3 fibre knob in complex with two copies of ...

SupramoleculeName: Human Adenovirus type 3 fibre knob in complex with two copies 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: Desmoglein 2

SupramoleculeName: 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: 21.025748 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NNTLWTGPKP EANCIIEYGK QNPDSKLTLI LVKNGGIVNG YVTLMGASDY VNTLFKNKNV SINVELYFDA TGHILPDSSS LKTDLELKY KQTADFSARG FMPSTTAYPF VLPNAGTHNE NYIFGQCYYK ASDGALFPLE VTVMLNKRLP DSRTSYVMTF L WSLNAGLA PETTQATLIT SPFTFSYIRE D

UniProtKB: Fiber protein

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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: 25.055029 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PVFTQDVFVG SVEELSAAHT LVMKINATDA DEPNTLNSKI SYRIVSLEPA YPPVFYLNKD TGEIYTTSVT LDREEHSSYT LTVEARDGN GEVTDKPVKQ AQVQIRILDV NDNIPVVENK VLEGMVEENQ VNVEVTRIKV FDADEIGSDN WLANFTFASG N EGGYFHIE ...String:
PVFTQDVFVG SVEELSAAHT LVMKINATDA DEPNTLNSKI SYRIVSLEPA YPPVFYLNKD TGEIYTTSVT LDREEHSSYT LTVEARDGN GEVTDKPVKQ AQVQIRILDV NDNIPVVENK VLEGMVEENQ VNVEVTRIKV FDADEIGSDN WLANFTFASG N EGGYFHIE TDAQTNEGIV TLIKEVDYEE MKNLDFSVIV ANKAAFHKSI RSKYKPTPIP IKVKVK

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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78925
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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