+Open data
-Basic information
Entry | Database: PDB / ID: 6z7q | |||||||||||||||
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Title | The atomic structure of the HAdVF-41 penton base in solution | |||||||||||||||
Components | Penton protein | |||||||||||||||
Keywords | VIRAL PROTEIN / HAdVF-41 / penton base / pentamer | |||||||||||||||
Function / homology | Adenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / Penton protein Function and homology information | |||||||||||||||
Biological species | Human adenovirus F serotype 41 | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 | 6z7q.cif.gz | 369.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z7q.ent.gz | 299.1 KB | Display | PDB format |
PDBx/mmJSON format | 6z7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z7q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6z7q_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6z7q_validation.xml.gz | 68.2 KB | Display | |
Data in CIF | 6z7q_validation.cif.gz | 99.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/6z7q ftp://data.pdbj.org/pub/pdb/validation_reports/z7/6z7q | HTTPS FTP |
-Related structure data
Related structure data | 11112MC 6z7nC 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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-Components
#1: Protein | Mass: 57142.160 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus F serotype 41 / Gene: L2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9QAH8 |
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-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 Details: The HAdVF-41 penton base was recombinantely expressed in Sf9 cells. Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.285 MDa / 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 |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was monodisperse with a preferred orientation in the vitrious ice. |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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 Details: Data were collected at a 30 degree tilt of the specimen stage due to a preferred orientation of the sample in the vitrified ice. |
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: 0.93 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 948 |
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: 1.18rc6_3830: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: per-micrograph CTF correction as well the initial per-particle CTF correction before 2D classification were performed in GCTF. Later per-particle CTF-refinement were performed in RELION 3.1-beta. Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 198491 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107110 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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