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- EMDB-1463: Three-dimensional structure of canine adenovirus serotype 2 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-1463
TitleThree-dimensional structure of canine adenovirus serotype 2 capsid
Map dataDensity map of canine adenovirus with C-terminal of protein IX fused with GFP protein
Sample
  • Sample: Canine adenovirus serotype 2
  • Virus: Canine adenovirus 2
Biological speciesCanine adenovirus 2
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 25.0 Å
AuthorsSchoehn G / El Bakkouri M / Fabry CM / Billet O / Estrozi LF / Le L / Curiel DT / Kajava AV / Ruigrok RW / Kremer EJ
CitationJournal: J Virol / Year: 2008
Title: Three-dimensional structure of canine adenovirus serotype 2 capsid.
Authors: Guy Schoehn / Majida El Bakkouri / Céline M S Fabry / Oliver Billet / Leandro F Estrozi / Long Le / David T Curiel / Andrey V Kajava / Rob W H Ruigrok / Eric J Kremer /
Abstract: There are more than 100 known adenovirus (AdV) serotypes, including 50 human serotypes. Because AdV-induced disease is relatively species specific, vectors derived from nonhuman serotypes may have ...There are more than 100 known adenovirus (AdV) serotypes, including 50 human serotypes. Because AdV-induced disease is relatively species specific, vectors derived from nonhuman serotypes may have wider clinical potential based, in part, on the lack of ubiquitous memory immunity. Whereas a few of the human serotype capsids have been studied at the structural level, none of the nonhuman serotypes has been analyzed. The basis laid by the analysis of human AdV (hAdV) has allowed us to determine and compare the three-dimensional structure of the capsid of canine serotype 2 (CAV-2) to that of hAdV serotype 5 (hAdV-5). We show that CAV-2 capsid has a smoother structure than the human serotypes. Many of the external loops found in the hAdV-5 penton base and the hexon, against which the antibody response is directed, are shorter or absent in CAV-2. On the other hand, the CAV-2 fiber appears to be more complex, with two bends in the shaft. An interesting difference between the human and canine viruses is that the C-terminal part of protein IX is in a different position, making an antenna sticking out of the CAV-2 capsid. The comparison between the two viruses allows the identification of sites that should be easy to modify on the CAV-2 capsid for altering tissue tropism or other biological activities.
History
DepositionJan 8, 2008-
Header (metadata) releaseJan 8, 2010-
Map releaseJan 8, 2010-
UpdateDec 25, 2013-
Current statusDec 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1463.png

Downloads & links

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Map

FileDownload / File: emd_1463.map.gz / Format: CCP4 / Size: 332.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of canine adenovirus with C-terminal of protein IX fused with GFP protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 447 pix.
= 1135.38 Å		2.54 Å/pix.
x 447 pix.
= 1135.38 Å		2.54 Å/pix.
x 447 pix.
= 1135.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2776.0 / Movie #1: 3000
Minimum - Maximum-19327.0 - 24394.0
Average (Standard dev.)548.379999999999995 (±3054.869999999999891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions447447447
Spacing447447447
CellA=B=C: 1135.38 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z447447447
origin x/y/z0.0000.0000.000
length x/y/z1135.3801135.3801135.380
α/β/γ90.00090.00090.000
start NX/NY/NZ29-50166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS447447447
D min/max/mean-19327.00024394.000548.380

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Supplemental data

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Sample components

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Entire : Canine adenovirus serotype 2

EntireName: Canine adenovirus serotype 2
Components
  • Sample: Canine adenovirus serotype 2
  • Virus: Canine adenovirus 2

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Supramolecule #1000: Canine adenovirus serotype 2

SupramoleculeName: Canine adenovirus serotype 2 / type: sample / ID: 1000
Details: The protein IX is fused with the GFP protein at his C termini
Number unique components: 1
Molecular weightExperimental: 150 MDa

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Supramolecule #1: Canine adenovirus 2

SupramoleculeName: Canine adenovirus 2 / type: virus / ID: 1 / NCBI-ID: 10514 / Sci species name: Canine adenovirus 2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Canis lupus familiaris (dog) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: Capsid / Diameter: 100 Å / T number (triangulation number): 25

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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: 7.4 / Details: Tris ph 7.4 NaCl 150 mM
StainingType: NEGATIVE / Details: Cryo EM
GridDetails: Quantifoil
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Zeiss / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 27500
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 20 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each negative
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT2, EM3DR2 / Number images used: 800

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