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- EMDB-3823: Structure of the truncated African cichlid nackednavirus icosahed... -

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Basic information

Entry
Database: EMDB / ID: 3823
TitleStructure of the truncated African cichlid nackednavirus icosahedral capsid
SampleRetro-transcribing viruses
SourceRetro-transcribing viruses / virus
Map dataStructure of the truncated African cichlid nackednavirus capsid
Methodsingle particle (icosahedral) reconstruction, at 9 Å resolution
AuthorsMattei S / Briggs JAG / Seitz S
CitationCell Host Microbe, 2017

Cell Host Microbe, 2017 StrPapers
Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses.
Chris Lauber / Stefan Seitz / Simone Mattei / Alexander Suh / Jürgen Beck / Jennifer Herstein / Jacob Börold / Walter Salzburger / Lars Kaderali / John A G Briggs / Ralf Bartenschlager

DateDeposition: Jul 21, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Sep 13, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.042
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3823.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.18 Å/pix.
= 604.16 Å
512 pix
1.18 Å/pix.
= 604.16 Å
512 pix
1.18 Å/pix.
= 604.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.18 Å
Density
Contour Level:0.042 (by author), 0.042 (movie #1):
Minimum - Maximum-0.03903188 - 0.10546035
Average (Standard dev.)0.0007083466 (0.0072973506)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin000
Limit511511511
Spacing512512512
CellA=B=C: 604.16 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.181.181.18
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z604.160604.160604.160
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0390.1050.001

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Supplemental data

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Sample components

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Entire Retro-transcribing viruses

EntireName: Retro-transcribing viruses
Details: truncated capsid variant (aa 1-146) lacking the C-terminal nucleic acid binding domain.
Number of components: 1

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Component #1: virus, Retro-transcribing viruses

VirusName: Retro-transcribing viruses / Class: VIRION
Details: truncated capsid variant (aa 1-146) lacking the C-terminal nucleic acid binding domain.
Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Retro-transcribing viruses / virus
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Host Species: Ophthalmotilapia ventralis
Shell #1Name of element: capsid / Diameter: 320 Å / T number(triangulation number): 3

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.2
Support film20 mA
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 288 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4000 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1018 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 360
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF

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