+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11778 | |||||||||
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Title | HAd7 knob in complex with 3 EC2-EC3 modules of DSG-2 | |||||||||
Map data | HAd7 knob in complex with three DSG-2 modules | |||||||||
Sample |
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Keywords | adenovirus / cell receptor / complex / 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 / 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 / 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 junction / viral capsid / cell-cell junction / cell adhesion / apical plasma membrane / symbiont entry into host cell / intracellular membrane-bounded organelle / calcium ion binding / host cell nucleus / cell surface / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human adenovirus B serotype 7 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Effantin G / Vassal-Stermann E | |||||||||
Funding support | France, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11778.map.gz | 96.4 MB | EMDB map data format | |
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Header (meta data) | emd-11778-v30.xml emd-11778.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11778_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_11778.png | 49.3 KB | ||
Filedesc metadata | emd-11778.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11778 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11778 | HTTPS FTP |
-Validation report
Summary document | emd_11778_validation.pdf.gz | 533.9 KB | Display | EMDB validaton report |
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Full document | emd_11778_full_validation.pdf.gz | 533.5 KB | Display | |
Data in XML | emd_11778_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_11778_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11778 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11778 | HTTPS FTP |
-Related structure data
Related structure data | 7agfMC 7aggC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11778.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HAd7 knob in complex with three DSG-2 modules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of...
Entire | Name: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2 |
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Components |
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-Supramolecule #1: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of...
Supramolecule | Name: Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 130 KDa |
-Supramolecule #2: Desmoglein-2
Supramolecule | Name: Desmoglein-2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Fiber
Supramolecule | Name: Fiber / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human adenovirus B serotype 7 |
-Macromolecule #1: Fiber
Macromolecule | Name: Fiber / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus B serotype 7 |
Molecular weight | Theoretical: 23.489217 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMGLTFNS NNICIDDNIN TLWTGVNPTT ANCQIMASSE SNDCKLILTL VKTGALVTAF VYVIGVSNDF NMLTTHKNIN FTAELFFDS TGNLLTSLSS LKTPLNHKSG QNMATGALTN AKGFMPSTTA YPFNVNSREK ENYIYGTCYY TASDHTAFPI D ISVMLNQR ...String: GSHMGLTFNS NNICIDDNIN TLWTGVNPTT ANCQIMASSE SNDCKLILTL VKTGALVTAF VYVIGVSNDF NMLTTHKNIN FTAELFFDS TGNLLTSLSS LKTPLNHKSG QNMATGALTN AKGFMPSTTA YPFNVNSREK ENYIYGTCYY TASDHTAFPI D ISVMLNQR ALNNETSYCI RVTWSWNTGV APEVQTSATT LVTSPFTFYY IREDD UniProtKB: Fiber |
-Macromolecule #2: Desmoglein-2
Macromolecule | Name: Desmoglein-2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 27.126275 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QGAMEVLDIN DNEPVFTQDV FVGSVEELSA AHTLVMKINA TDADEPNTLN SKISYRIVSL EPAYPPVFYL NKDTGEIYTT SVTLDREEH SSYTLTVEAR DGNGEVTDKP VKQAQVQIRI LDVNDNIPVV ENKVLEGMVE ENQVNVEVTR IKVFDADEIG S DNWLANFT ...String: QGAMEVLDIN DNEPVFTQDV FVGSVEELSA AHTLVMKINA TDADEPNTLN SKISYRIVSL EPAYPPVFYL NKDTGEIYTT SVTLDREEH SSYTLTVEAR DGNGEVTDKP VKQAQVQIRI LDVNDNIPVV ENKVLEGMVE ENQVNVEVTR IKVFDADEIG S DNWLANFT FASGNEGGYF HIETDAQTNE GIVTLIKEVD YEEMKNLDFS VIVANKAAFH KSIRSKYKPT PIPIKVKVKN VK EGI UniProtKB: Desmoglein-2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |