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- PDB-2c9f: THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON DODECAHEDRON -

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Basic information

Entry
Database: PDB / ID: 2c9f
TitleTHE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON DODECAHEDRON
Components
  • FIBER
  • PENTON PROTEIN
KeywordsVIRUS/VIRAL PROTEIN / VIRUS-VIRAL PROTEIN COMPLEX / DODECAHEDRON / PENTON / FIBRE
Function / homology
Function and homology information


T=25 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / viral capsid / clathrin-dependent endocytosis of virus by host cell / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Adenovirus penton base protein / Adenovirus penton base protein / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Fiber protein / Penton protein / L5 fiber
Similarity search - Component
Biological speciesHUMAN ADENOVIRUS TYPE 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.5 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 1.0Mar 2, 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 1.4Oct 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 1.5Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.6May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as assembly
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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
S: FIBER
T: FIBER
U: FIBER
V: FIBER
W: FIBER


Theoretical massNumber of molelcules
Total (without water)302,18610
Polymers302,18610
Non-polymers00
Water00
1
A: PENTON PROTEIN
B: PENTON PROTEIN
C: PENTON PROTEIN
D: PENTON PROTEIN
E: PENTON PROTEIN
S: FIBER
T: FIBER
U: FIBER
V: FIBER
W: FIBER
x 12


Theoretical massNumber of molelcules
Total (without water)3,626,229120
Polymers3,626,229120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
2
A: PENTON PROTEIN
S: FIBER


  • icosahedral asymmetric unit
  • 60.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)60,4372
Polymers60,4372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • icosahedral pentamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: PENTON PROTEIN
E: PENTON PROTEIN
S: FIBER
W: FIBER

A: PENTON PROTEIN
B: PENTON PROTEIN
S: FIBER
T: FIBER

C: PENTON PROTEIN
D: PENTON PROTEIN
U: FIBER
V: FIBER


  • icosahedral 23 hexamer
  • 363 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)362,62312
Polymers362,62312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
5
A: PENTON PROTEIN
S: FIBER


  • icosahedral asymmetric unit, std point frame
  • 60.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)60,4372
Polymers60,4372
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 TYPE 2 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P03276
#2: Protein/peptide
FIBER / N-TERMINAL PEPTIDE OF THE FIBER


Mass: 2218.468 Da / Num. of mol.: 5 / Fragment: RESIDUES 1-19 / Source method: isolated from a natural source / Details: VIRION COMPONENT IV, FIBER PROTEIN / Source: (natural) HUMAN ADENOVIRUS TYPE 2 / References: UniProt: Q64831, UniProt: P03275*PLUS

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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 ENTIRE DODECAHEDRAL PARTICLE / 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: FEI/PHILIPS CM200T
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 40930 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 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: 12
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Bsoft3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: AMPLITUDE, PHASE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: POLAR FOURIER TRANSFROM, FOURIER BESSELS RECONSTRUCTION
Resolution: 16.5 Å / Num. of particles: 1849 / Nominal pixel size: 1.84 Å / Actual pixel size: 1.71 Å
Magnification calibration: COMPARISON WITH THE ATOMIC STRUCTURE
Details: TO RECONSTITUTE THE ENTIRE DODECAHEDRON, YOU MUST APPLY THE 12 MATRICES TO THE ENTIRE PENTAMER.
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: 16.5 Å
Refinement stepCycle: LAST / Highest resolution: 16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18025 0 0 0 18025

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