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- PDB-7agf: HAd7 knob in complex with 3 EC2-EC3 modules of DSG-2 -

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Basic information

Entry
Database: PDB / ID: 7agf
TitleHAd7 knob in complex with 3 EC2-EC3 modules of DSG-2
Components
  • Desmoglein-2
  • Fiber
KeywordsVIRAL PROTEIN / adenovirus / cell receptor / complex
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 / Apoptotic cleavage of cell adhesion proteins ...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 / Apoptotic cleavage of cell adhesion proteins / adhesion receptor-mediated virion attachment to host cell / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of heart rate by cardiac conduction / RHOG GTPase cycle / intercalated disc / maternal process involved in female pregnancy / lateral plasma membrane / RAC3 GTPase cycle / RAC2 GTPase cycle / cell adhesion molecule binding / response to progesterone / cell-cell adhesion / viral capsid / cell-cell junction / cell junction / cell adhesion / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / host cell nucleus / calcium ion binding / 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 / Cadherin conserved site ...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 / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
Fiber protein / Desmoglein-2 / Fiber
Similarity search - Component
Biological speciesHuman adenovirus B serotype 7
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsEffantin, G. / Vassal-Stermann, E. / Fender, P.
Funding support France, 1items
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Fiber
D: Desmoglein-2
E: Desmoglein-2
F: Desmoglein-2
B: Fiber
C: Fiber


Theoretical massNumber of molelcules
Total (without water)151,8466
Polymers151,8466
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_1ens_2chain "D"
d_2ens_2chain "E"
d_3ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPASPF1 - 198
d_21ens_1ASPASPE1 - 198
d_31ens_1ASPASPA1 - 198
d_11ens_2VALVALB1 - 231
d_21ens_2VALVALC1 - 231
d_31ens_2VALVALD1 - 231

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.500136271588, 0.865946709357, 7.99786116202E-5), (-0.8659465951, -0.500136153125, -0.000568130907481), (-0.000451970894669, -0.000353400080254, 0.999999835415)16.5014492447, 153.839616243, 0.0546696301126
2given(-0.499568205797, -0.866274553151, 7.94987289521E-5), (0.866274277552, -0.499567968969, 0.000848782932857), (-0.000695564037325, 0.000492892670867, 0.999999636624)141.457033235, 62.5692980224, 0.0156991767547
3given(-0.500775551654, -0.865577005667, 0.000542334305817), (0.865577033979, -0.500775729818, -0.000258210903232), (0.000495089278251, 0.000340126412345, 0.9999998196)141.455740462, 62.7469219639, -0.027285756196
4given(-0.498183090378, 0.867070852808, 0.00132086030597), (-0.867071794439, -0.498181887993, -0.00114444937255), (-0.000334290012446, -0.0017154260409, 0.999998472781)16.1832566801, 153.811041387, 0.193899438733

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Components

#1: Protein Fiber / / Fiber protein / L5 fiber protein


Mass: 23489.217 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B serotype 7 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EY45, UniProt: P15141*PLUS
#2: Protein Desmoglein-2 / / Cadherin family member 5 / HDGC


Mass: 27126.275 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSG2, CDHF5 / Production host: Homo sapiens (human) / 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 7 knob in complex with 2 EC2 EC3 modules of DSG-2COMPLEXall0MULTIPLE SOURCES
2Desmoglein-2COMPLEX#21RECOMBINANT
3FiberCOMPLEX#11RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Human adenovirus B serotype 710519
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding 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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58219 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 47.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610269
ELECTRON MICROSCOPYf_angle_d0.84614010
ELECTRON MICROSCOPYf_dihedral_angle_d6.5741365
ELECTRON MICROSCOPYf_chiral_restr0.0541653
ELECTRON MICROSCOPYf_plane_restr0.0051815
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FELECTRON MICROSCOPYNCS constraints0.000702045966641
ens_1d_3FELECTRON MICROSCOPYNCS constraints0.000714009299312
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.000708597483044
ens_2d_3BELECTRON MICROSCOPYNCS constraints0.000718493983979

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