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- EMDB-8371: Three-dimensional reconstruction of bat adenovirus C isolate 250-A -

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Basic information

Entry
Database: EMDB / ID: EMD-8371
TitleThree-dimensional reconstruction of bat adenovirus C isolate 250-A
Map dataThe bat adenovirus isolate 250-A reconstruction by cryo-EM
Sample
  • Virus: Bat adenovirus
Biological speciesBat adenovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 17.9 Å
AuthorsHackenbrack NM / Hafenstein SL
CitationJournal: Science / Year: 2010
Title: Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks.
Authors: Hongrong Liu / Lei Jin / Sok Boon S Koh / Ivo Atanasov / Stan Schein / Lily Wu / Z Hong Zhou /
Abstract: Construction of a complex virus may involve a hierarchy of assembly elements. Here, we report the structure of the whole human adenovirus virion at 3.6 angstroms resolution by cryo-electron ...Construction of a complex virus may involve a hierarchy of assembly elements. Here, we report the structure of the whole human adenovirus virion at 3.6 angstroms resolution by cryo-electron microscopy (cryo-EM), revealing in situ atomic models of three minor capsid proteins (IIIa, VIII, and IX), extensions of the (penton base and hexon) major capsid proteins, and interactions within three protein-protein networks. One network is mediated by protein IIIa at the vertices, within group-of-six (GOS) tiles--a penton base and its five surrounding hexons. Another is mediated by ropes (protein IX) that lash hexons together to form group-of-nine (GON) tiles and bind GONs to GONs. The third, mediated by IIIa and VIII, binds each GOS to five surrounding GONs. Optimization of adenovirus for cancer and gene therapy could target these networks.
History
DepositionSep 9, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 5, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8371.png

Downloads & links

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Map

FileDownload / File: emd_8371.map.gz / Format: CCP4 / Size: 349.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe bat adenovirus isolate 250-A reconstruction by cryo-EM
Voxel sizeX=Y=Z: 2.33 Å
Density
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-5.7268176 - 6.1820703
Average (Standard dev.)0.000000001399634 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-225-225-225
Dimensions451451451
Spacing451451451
CellA=B=C: 1050.83 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z451451451
origin x/y/z0.0000.0000.000
length x/y/z1050.8301050.8301050.830
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS451451451
D min/max/mean-5.7276.1820.000

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Supplemental data

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Sample components

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Entire : Bat adenovirus

EntireName: Bat adenovirus
Components
  • Virus: Bat adenovirus

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Supramolecule #1: Bat adenovirus

SupramoleculeName: Bat adenovirus / type: virus / ID: 1 / Parent: 0
Details: Bat adenovirus C isolate 250-A was isolated from Corynorhinus rafinesquii at the Mammoth Cave National Park in Kentucky, USA
NCBI-ID: 740971 / Sci species name: Bat adenovirus / Sci species strain: C / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Plecotus rafinesquii (Rafinesque's big-eared bat)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMTris-HClTristris hydrochloride
100.0 mMNaClSodium chloridesodium chloride
10.0 mMMgCl2magnesium chloride
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 7.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 2e-06 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: GATAN CRYOPLUNGE 3
DetailsTissue from Corynorhinus rafinesquii was homogenized, clarified, and then used to infect Vero E6 cells. The supernatant was harvested and spun on a cesium chloride step gradient. Full particles were harvested, dialyzed, and concentrated.

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Electron microscopy

MicroscopeJEOL 2100
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 383 / Average electron dose: 10.0 e/Å2

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Image processing

Particle selectionNumber selected: 1592
CTF correctionSoftware - Name: Auto3DEM
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: COMMON LINE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 17.9 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1109

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