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- EMDB-2273: Cryo-EM structures of two intermediates provide insight into aden... -

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Basic information

Entry
Database: EMDB / ID: EMD-2273
TitleCryo-EM structures of two intermediates provide insight into adenovirus assembly and disassembly
Map dataAssembly intermediate of Bovine Adenovirus type 3
Sample
  • Sample: Bovine Adenovirus type 3
  • Virus: Bovine adenovirus 3
KeywordsAdenovirus / assembly intermediate
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral process / endocytosis involved in viral entry into host cell / viral capsid / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell
Similarity search - Function
: / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain ...: / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Penton protein / Pre-hexon-linking protein VIII / Hexon protein / PIX
Similarity search - Component
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 6, 2013-
Header (metadata) releaseFeb 6, 2013-
Map releaseJan 22, 2014-
UpdateMar 2, 2016-
Current statusMar 2, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3zif
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3zif
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2273-B1P.jpg

Downloads & links

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Map

FileDownload / File: emd_2273.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAssembly intermediate of Bovine Adenovirus type 3
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 9.0 / Movie #1: 9
Minimum - Maximum-25.395584110000001 - 34.82930374
Average (Standard dev.)0.15943675 (±3.83022094)
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-25.39634.8290.159

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Supplemental data

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Sample components

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Entire : Bovine Adenovirus type 3

EntireName: Bovine Adenovirus type 3
Components
  • Sample: Bovine Adenovirus type 3
  • Virus: Bovine adenovirus 3

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Supramolecule #1000: Bovine Adenovirus type 3

SupramoleculeName: Bovine Adenovirus type 3 / type: sample / ID: 1000 / Oligomeric state: 60-mer / 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 (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 / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 125390 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateFeb 2, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 1.16 µm / Number real images: 1275 / Average electron dose: 25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Software - Name: ISAFs / Number images used: 11910

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