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- EMDB-2272: Cryo-EM structures of two intermediates provide insight into aden... -

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Basic information

Entry
Database: EMDB / ID: EMD-2272
TitleCryo-EM structures of two intermediates provide insight into adenovirus assembly and disassembly
Map dataAveraged hexon
Sample
  • Sample: Disassembly and assembly intermediates of bovine adenovirus type 3
  • Virus: Bovine adenovirus 3
KeywordsAdenovirus / intermediate
Biological speciesBovine adenovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCheng L / Huang X / Li X / Xiong W / Sun W / Yang C / Zhang K / Wang Y / Liu H / Ji G ...Cheng L / Huang X / Li X / Xiong W / Sun W / Yang C / Zhang K / Wang Y / Liu H / Ji G / Sun F / Zheng C / Zhu P
CitationJournal: Virology / Year: 2014
Title: Cryo-EM structures of two bovine adenovirus type 3 intermediates.
Authors: Lingpeng Cheng / Xiaoxing Huang / Xiaomin Li / Wei Xiong / Wei Sun / Chongwen Yang / Kai Zhang / Ying Wang / Hongrong Liu / Xiaojun Huang / Gang Ji / Fei Sun / Congyi Zheng / Ping Zhu /
Abstract: Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained ...Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level.
History
DepositionJan 4, 2013-
Header (metadata) releaseJan 16, 2013-
Map releaseJan 22, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2272.png

Downloads & links

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Map

FileDownload / File: emd_2272.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged hexon
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 800 pix.
= 928. Å		1.16 Å/pix.
x 800 pix.
= 928. Å		1.16 Å/pix.
x 800 pix.
= 928. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0 / Movie #1: 10
Minimum - Maximum-20.23997688 - 28.975549699999998
Average (Standard dev.)0.19486694 (±3.31325245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-412-412-412
Dimensions800800800
Spacing800800800
CellA=B=C: 928.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z928.000928.000928.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-412-412-412
NC/NR/NS800800800
D min/max/mean-20.24028.9760.195

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Supplemental data

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Sample components

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Entire : Disassembly and assembly intermediates of bovine adenovirus type 3

EntireName: Disassembly and assembly intermediates of bovine adenovirus type 3
Components
  • Sample: Disassembly and assembly intermediates of bovine adenovirus type 3
  • Virus: Bovine adenovirus 3

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Supramolecule #1000: Disassembly and assembly intermediates of bovine adenovirus type 3

SupramoleculeName: Disassembly and assembly intermediates of bovine adenovirus type 3
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Bovine adenovirus 3

SupramoleculeName: Bovine adenovirus 3 / type: virus / ID: 1 / NCBI-ID: 10510 / Sci species name: Bovine adenovirus 3 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bos taurus (domestic cattle) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJan 2, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 125390 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Software - Name: ISAFs / Number images used: 28505

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