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Yorodumi- EMDB-4608: Human Adenovirus type 3 fiber knob in complex with one copy of De... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4608 | |||||||||
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Title | Human Adenovirus type 3 fiber knob in complex with one copy of Desmoglein-2 | |||||||||
Map data | Human Adenovirus type 3 fiber knob in complex with one DSG-2 | |||||||||
Sample |
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Keywords | virus 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 / 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 | Human adenovirus B serotype 3 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Effantin G | |||||||||
Funding support | France, 1 items
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Citation | Journal: 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 |
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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_4608.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-4608-v30.xml emd-4608.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4608_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_4608.png | 105.5 KB | ||
Filedesc metadata | emd-4608.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4608 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4608 | HTTPS FTP |
-Validation report
Summary document | emd_4608_validation.pdf.gz | 292.5 KB | Display | EMDB validaton report |
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Full document | emd_4608_full_validation.pdf.gz | 291.7 KB | Display | |
Data in XML | emd_4608_validation.xml.gz | 9.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4608 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4608 | HTTPS FTP |
-Related structure data
Related structure data | 6qntMC 4609C 6qnuC C: citing same article (ref.) M: atomic model generated by this map |
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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_4608.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human Adenovirus type 3 fiber knob in complex with one DSG-2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 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 3 fibre knob in complex with one copy of De...
Entire | Name: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2 |
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Components |
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-Supramolecule #1: Human Adenovirus type 3 fibre knob in complex with one copy of De...
Supramolecule | Name: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 96 KDa |
-Supramolecule #2: Human Adenovirus type 3 fibre knob in complex with one copy of De...
Supramolecule | Name: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2 type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human adenovirus B serotype 3 |
-Supramolecule #3: Human Adenovirus type 3 fibre knob in complex with one copy of De...
Supramolecule | Name: Human Adenovirus type 3 fibre knob in complex with one copy of Desmoglein 2 type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Fiber protein
Macromolecule | Name: Fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus B serotype 3 |
Molecular weight | Theoretical: 20.95467 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: NNTLWTGPKP EANCIIEYGK QNPDSKLTLI LVKNGGIVNG YVTLMGASDY VNTLFKNKNV SINVELYFDA TGHILPDSSS LKTDLELKY KQTADFSARG FMPSTTAYPF VLPNGTHNEN YIFGQCYYKA SDGALFPLEV TVMLNKRLPD SRTSYVMTFL W SLNAGLAP ETTQATLITS PFTFSYIRED UniProtKB: Fiber protein |
-Macromolecule #2: Desmoglein-2
Macromolecule | Name: Desmoglein-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.268219 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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: 35.0 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 |