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Yorodumi- EMDB-4609: Human Adenovirus type 3 fiber knob in complex with two copies of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4609 | |||||||||
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Title | Human Adenovirus type 3 fiber knob in complex with two copies of Desmoglein-2 | |||||||||
Map data | ||||||||||
Sample |
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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 | |||||||||
Biological species | Human adenovirus B serotype 3 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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_4609.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-4609-v30.xml emd-4609.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4609_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_4609.png | 127.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4609 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4609 | HTTPS FTP |
-Related structure data
Related structure data | 6qnuMC 4608C 6qntC 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_4609.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 two copies of ...
Entire | Name: Human Adenovirus type 3 fibre knob in complex with two copies of Desmoglein 2 |
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Components |
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-Supramolecule #1: Human Adenovirus type 3 fibre knob in complex with two copies of ...
Supramolecule | Name: Human Adenovirus type 3 fibre knob in complex with two copies of Desmoglein 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Experimental: 116 KDa |
-Supramolecule #2: Human Adenovirus type 3 fibre knob in complex with two copies of ...
Supramolecule | Name: Human Adenovirus type 3 fibre knob in complex with two copies of Desmoglein 2 type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human adenovirus B serotype 3 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: Desmoglein 2
Supramolecule | Name: Desmoglein 2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-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: 21.025748 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: NNTLWTGPKP EANCIIEYGK QNPDSKLTLI LVKNGGIVNG YVTLMGASDY VNTLFKNKNV SINVELYFDA TGHILPDSSS LKTDLELKY KQTADFSARG FMPSTTAYPF VLPNAGTHNE NYIFGQCYYK ASDGALFPLE VTVMLNKRLP DSRTSYVMTF L WSLNAGLA PETTQATLIT SPFTFSYIRE D |
-Macromolecule #2: Desmoglein-2
Macromolecule | Name: Desmoglein-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.055029 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |