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- PDB-2c9g: THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON BASE DODEC... -

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Entry
Database: PDB / ID: 2c9g
TitleTHE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON BASE DODECAHEDRON
ComponentsPENTON PROTEIN
KeywordsVIRUS/VIRAL PROTEIN / VIRUS-VIRAL PROTEIN COMPLEX / DODECAHEDRON / PENTON / FIBRE / LATE PROTEIN
Function / homologyAdenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / structural molecule activity / virion attachment to host cell / Penton protein
Function and homology information
Biological speciesHUMAN ADENOVIRUS 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsFuschiotti, P. / Schoehn, G. / Fender, P. / Fabry, C.M.S. / Hewat, E.A. / Chroboczek, J. / Ruigrok, R.W.H. / Conway, J.F.
CitationJournal: 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
DepositionDec 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Aug 30, 2017Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.5Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.6Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: PENTON PROTEIN
B: PENTON PROTEIN
C: PENTON PROTEIN
D: PENTON PROTEIN
E: PENTON PROTEIN


Theoretical massNumber of molelcules
Total (without water)291,0935
Polymers291,0935
Non-polymers00
Water0
1
A: PENTON PROTEIN
B: PENTON PROTEIN
C: PENTON PROTEIN
D: PENTON PROTEIN
E: PENTON PROTEIN
x 12


Theoretical massNumber of molelcules
Total (without water)3,493,12160
Polymers3,493,12160
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation12
2
A: PENTON PROTEIN


  • icosahedral asymmetric unit
  • 58.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)58,2191
Polymers58,2191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • icosahedral pentamer
TypeNameSymmetry operationNumber
point symmetry operation1
4
A: PENTON PROTEIN
x 6


  • icosahedral 23 hexamer
  • 349 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)349,3126
Polymers349,3126
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5
A: PENTON PROTEIN


  • icosahedral asymmetric unit, std point frame
  • 58.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)58,2191
Polymers58,2191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
PENTON PROTEIN / / VIRION COMPONENT III / PENTON BASE PROTEIN / PIII


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN ADENOVIRUS TYPE 3 / Type: VIRUS
Buffer solutionpH: 6.6
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 51020 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 1.4 mm
Specimen holderTemperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 14
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1EM3DR23D reconstruction
2PFTsearch3D reconstruction
CTF correctionDetails: AMPLITUDE, PHASE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: 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 buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: RFACTOR, CORRELATION COEFFICIENT / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
RefinementHighest resolution: 9.3 Å
Refinement stepCycle: LAST / Highest resolution: 9.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17840 0 0 0 17840

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