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- PDB-6qnt: Human Adenovirus type 3 fiber knob in complex with one copy of De... -

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Basic information

Entry
Database: PDB / ID: 6qnt
TitleHuman Adenovirus type 3 fiber knob in complex with one copy of Desmoglein-2
Components
  • Desmoglein-2
  • Fiber protein
KeywordsVIRAL PROTEIN / virus receptor / adenovirus / vector
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 / Adenovirus pIV-related, attachment domain / : / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / 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 ...Desmosomal cadherin / Adenovirus pIV-related, attachment domain / : / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fiber protein / Desmoglein-2
Similarity search - Component
Biological speciesHuman adenovirus B serotype 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsEffantin, G.
Funding support France, 1items
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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Other / Category: atom_sites / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2Sep 30, 2020Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.phase_plate
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Fiber protein
D: Desmoglein-2


Theoretical massNumber of molelcules
Total (without water)86,1324
Polymers86,1324
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-35 kcal/mol
Surface area32420 Å2
MethodPISA

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Components

#1: Protein Fiber protein / SPIKE / Protein IV


Mass: 20954.670 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B serotype 3 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: P04501
#2: Protein Desmoglein-2 / Cadherin family member 5 / HDGC


Mass: 23268.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSG2, CDHF5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14126

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2COMPLEXall0RECOMBINANT
2Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2COMPLEX#11RECOMBINANT
3Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2COMPLEX#21RECOMBINANT
Molecular weightValue: 0.096 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Human adenovirus B serotype 345659
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139958 / Symmetry type: POINT

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