+Open data
-Basic information
Entry | Database: PDB / ID: 6z7n | |||||||||||||||
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Title | The atomic structure of HAdV-F41 at pH 7.4 | |||||||||||||||
Components |
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Keywords | VIRUS / HAdV-F41 / virion / icosahedral | |||||||||||||||
Function / homology | Function and homology information hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / virion component => GO:0044423 / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / endocytosis involved in viral entry into host cell ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / virion component => GO:0044423 / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding Similarity search - Function | |||||||||||||||
Biological species | Human adenovirus 41 | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.77 Å | |||||||||||||||
Authors | Carlson, L.-A. / Rafie, K. | |||||||||||||||
Funding support | Sweden, 4items
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Citation | Journal: Sci Adv / Year: 2021 Title: The structure of enteric human adenovirus 41-A leading cause of diarrhea in children. Authors: K Rafie / A Lenman / J Fuchs / A Rajan / N Arnberg / L-A Carlson / Abstract: Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and ...Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here, we present the first structure of an enteric HAdV-HAdV-F41-determined by cryo-electron microscopy to a resolution of 3.8 Å. The structure reveals extensive alterations to the virion exterior as compared to nonenteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of core protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation of enteric HAdVs to a fundamentally different tissue tropism. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6z7n.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6z7n.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 6z7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/6z7n ftp://data.pdbj.org/pub/pdb/validation_reports/z7/6z7n | HTTPS FTP |
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-Related structure data
Related structure data | 11108MC 6z7qC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 28 molecules 0123456789ABCDEFGHIJKLMNPQRS
#1: Protein | Mass: 29170.145 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: P16139 #2: Protein | Mass: 104064.234 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: P11820 #3: Protein | | Mass: 57142.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: Q9QAH8 #4: Protein | | Mass: 39843.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: B5SNS2 #6: Protein | Mass: 13617.179 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: B5SNR3, UniProt: P32539*PLUS |
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-Pre-hexon-linking protein ... , 2 types, 3 molecules OTU
#5: Protein | Mass: 64825.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: Q67716 |
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#7: Protein | Mass: 25330.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 / References: UniProt: P11822 |
-Protein/peptide , 3 types, 5 molecules XWVZY
#8: Protein/peptide | Mass: 899.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: belongs to one of the two fibre proteins: P14267 or P16883 Source: (natural) Human adenovirus 41 / Cell line: A549 | ||
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#9: Protein/peptide | Mass: 869.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 #10: Protein/peptide | | Mass: 528.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 41 / Cell line: A549 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human adenovirus 41 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Human adenovirus 41 |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION |
Natural host | Organism: Homo sapiens |
Virus shell | Diameter: 900 nm |
Buffer solution | pH: 7.4 Details: PBS buffer made from comemrcial PBS tablets Medicargo, PBS tablets, 09-9400-100 |
Specimen | Conc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 295.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.03 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6929 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.18_3845: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 25667 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19472 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5TX1 Accession code: 5TX1 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.77 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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