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Yorodumi- PDB-2c9g: THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON BASE DODEC... -
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-Basic information
Entry | Database: PDB / ID: 2c9g | ||||||
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Title | THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON BASE DODECAHEDRON | ||||||
Components | PENTON PROTEIN | ||||||
Keywords | VIRUS/VIRAL PROTEIN / VIRUS-VIRAL PROTEIN COMPLEX / DODECAHEDRON / PENTON / FIBRE / LATE PROTEIN | ||||||
Function / homology | Adenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / Penton protein Function and homology information | ||||||
Biological species | HUMAN ADENOVIRUS 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.3 Å | ||||||
Authors | Fuschiotti, P. / Schoehn, G. / Fender, P. / Fabry, C.M.S. / Hewat, E.A. / Chroboczek, J. / Ruigrok, R.W.H. / Conway, J.F. | ||||||
Citation | Journal: J Mol Biol / Year: 2006 Title: Structure of the dodecahedral penton particle from human adenovirus type 3. Authors: P Fuschiotti / G Schoehn / P Fender / C M S Fabry / E A Hewat / J Chroboczek / R W H Ruigrok / J F Conway / Abstract: The sub-viral dodecahedral particle of human adenovirus type 3, composed of the viral penton base and fiber proteins, shares an important characteristic of the entire virus: it can attach to cells ...The sub-viral dodecahedral particle of human adenovirus type 3, composed of the viral penton base and fiber proteins, shares an important characteristic of the entire virus: it can attach to cells and penetrate them. Structure determination of the fiberless dodecahedron by cryo-electron microscopy to 9 Angstroms resolution reveals tightly bound pentamer subunits, with only minimal interfaces between penton bases stabilizing the fragile dodecahedron. The internal cavity of the dodecahedron is approximately 80 Angstroms in diameter, and the interior surface is accessible to solvent through perforations of approximately 20 Angstroms diameter between the pentamer towers. We observe weak density beneath pentamers that we attribute to a penton base peptide including residues 38-48. The intact amino-terminal domain appears to interfere with pentamer-pentamer interactions and its absence by mutation or proteolysis is essential for dodecamer assembly. Differences between the 9 Angstroms dodecahedron structure and the adenovirus serotype 2 (Ad2) crystallographic model correlate closely with differences in sequence. The 3D structure of the dodecahedron including fibers at 16 Angstroms resolution reveals extra density on the top of the penton base that can be attributed to the fiber N terminus. The fiber itself exhibits striations that correlate with features of the atomic structure of the partial Ad2 fiber and that represent a repeat motif present in the amino acid sequence. These new observations offer important insights into particle assembly and stability, as well as the practicality of using the dodecahedron in targeted drug delivery. The structural work provides a sound basis for manipulating the properties of this particle and thereby enhancing its value for such therapeutic use. | ||||||
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 | 2c9g.cif.gz | 443.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c9g.ent.gz | 360.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c9g_validation.pdf.gz | 884.4 KB | Display | wwPDB validaton report |
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Full document | 2c9g_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2c9g_validation.xml.gz | 90.8 KB | Display | |
Data in CIF | 2c9g_validation.cif.gz | 130.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9g ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9g | HTTPS FTP |
-Related structure data
Related structure data | 1178MC 1179C 2c9fC 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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2 |
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3 |
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4 |
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5 |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 58218.684 Da / Num. of mol.: 5 / Fragment: RESIDUES 49-571 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN ADENOVIRUS 2 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P03276 |
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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 TYPE 3 / Type: VIRUS |
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Buffer solution | pH: 6.6 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 2010F |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51020 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 1.4 mm |
Specimen holder | Temperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 14 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: AMPLITUDE, PHASE | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: POLAR FOURIER TRANSFROM, FOURIER BESSELS RECONSTRUCTION Resolution: 9.3 Å / Num. of particles: 1849 / Nominal pixel size: 1.4 Å / Actual pixel size: 1.372 Å Magnification calibration: COMPARISON WITH THE ATOMIC STRUCTURE Details: TO RECONSTITUTE THE ENTIRE PENTON BASE DODECAHEDRAL PARTICLE, YOU MUST APPLY THE 12 MATRICES TO THE ENTIRE PENTAMER IN THIS ENTRY. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: RFACTOR, CORRELATION COEFFICIENT / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Refinement | Highest resolution: 9.3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.3 Å
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