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- EMDB-1178: Structure of the dodecahedral penton particle from human adenovir... -

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Basic information

Entry
Database: EMDB / ID: EMD-1178
TitleStructure of the dodecahedral penton particle from human adenovirus type 3.
Map dataThe pixel size has been calibrated using the X-ray structure of adenovirus 2 penton base. Accession number 1X9P
Sample
  • Sample: adenovirus 3 penton base dodecahedron
  • Protein or peptide: Ad3 penton base
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 3
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 9.3 Å
AuthorsFuschiotti P / Schoehn G / Fender P / Fabry CMS / Hewat EA / Chroboczek J
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
DepositionNov 4, 2005-
Header (metadata) releaseNov 4, 2005-
Map releaseNov 7, 2005-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 110
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 110
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2c9g
  • Surface level: 110
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2c9g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1178.gif

Downloads & links

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Map

FileDownload / File: emd_1178.map.gz / Format: CCP4 / Size: 40.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThe pixel size has been calibrated using the X-ray structure of adenovirus 2 penton base. Accession number 1X9P
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 279 pix.
= 382.23 Å		1.37 Å/pix.
x 279 pix.
= 382.23 Å		1.37 Å/pix.
x 279 pix.
= 382.23 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 91.900000000000006 / Movie #1: 110
Minimum - Maximum-335.0 - 509.0
Average (Standard dev.)3.05461431 (±52.415409089999997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-139-139-139
Dimensions279279279
Spacing279279279
CellA=B=C: 382.23 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.371.371.37
M x/y/z279279279
origin x/y/z0.0000.0000.000
length x/y/z382.230382.230382.230
α/β/γ90.00090.00090.000
start NX/NY/NZ-77-770
NX/NY/NZ15515578
MAP C/R/S123
start NC/NR/NS-139-139-139
NC/NR/NS279279279
D min/max/mean-335.000509.0003.055

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Supplemental data

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Sample components

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Entire : adenovirus 3 penton base dodecahedron

EntireName: adenovirus 3 penton base dodecahedron
Components
  • Sample: adenovirus 3 penton base dodecahedron
  • Protein or peptide: Ad3 penton base

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Supramolecule #1000: adenovirus 3 penton base dodecahedron

SupramoleculeName: adenovirus 3 penton base dodecahedron / type: sample / ID: 1000
Details: The penton base was expressed in baculovirus abd the penton base self-assemble into dodecahedrons
Oligomeric state: 12 pentamers / Number unique components: 1
Molecular weightExperimental: 3.5 MDa

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Macromolecule #1: Ad3 penton base

MacromoleculeName: Ad3 penton base / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Oligomeric state: dodecamer of pentamer / Recombinant expression: Yes
Source (natural)Organism: Human adenovirus 3 / synonym: human adenovirus 3
Molecular weightExperimental: 60 KDa / Theoretical: 60 KDa
Recombinant expressionOrganism: unidentified baculovirus / Recombinant plasmid: pAcUW31

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 6.6 / Details: 25 mM phosphate buffer at pH 6.6
StainingType: NEGATIVE
Details: Quantifoil R2 1 grids (Quantifoil Micro Tools GmbH, Germany) were loaded with 4 ul of sample at 1 mg ml, blotted and rapidly frozen in liquid ethane within a liquid nitrogen bath using a Zeiss cryoplunger
GridDetails: Quantifoil R2/1 grids
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Zeiss cryoplunger

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 14
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51100 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

DetailsThe particles were selected using X3d
CTF correctionDetails: each negative or each focal pair
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: PFT EM3DR PFT2 EM3DR2 / Number images used: 1849

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